Personalized site-specific immunomodulation

ABSTRACT

The invention provides methods of treating inflammation in a specific organ or tissue of an individual. The method involves determining whether the individual has previously been infected with at least one pathogen that is pathogenic in the specific organ or tissue; and administering to the individual an anti-inflammatory composition comprising antigenic determinants, the antigenic determinants selected or formulated so that together they are specific for the at least one pathogen. The pathogen may be an endogenous or exogenous pathogen, and may further be a bacterial pathogen, a viral pathogen, a fungal pathogen, a protozoan pathogen, or a helminth pathogen.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation-in-Part application of U.S. application Ser. No. 13/359,441 filed Jan. 26, 2012; which application is a Continuation-in-Part application of PCT Application Serial No. PCT/CA2011/000851 filed Jul. 26, 2011; which application is: (I) a Continuation-in-Part application of U.S. application Ser. No. 13/019,208 filed Feb. 1, 2011; which application is a Continuation-in-Part application of U.S. application Ser. No. 12/843,296 filed on Jul. 26, 2010; and (II) pursuant to 35 U.S.C. §119 (e), claims priority to the filing date of U.S. Provisional Patent Application Ser. No. 61/411,371 filed Nov. 8, 2010 and U.S. Provisional Patent Application Ser. No. 61/500,836 filed Jun. 24, 2011. The disclosures of all of the applications listed in this paragraph [0001] are herein incorporated by reference.

FIELD OF THE INVENTION

In various aspects, the invention relates to immunological therapies for treating a condition characterized by inflammation. In alternative embodiments, the invention provides methods of personalizing immunomodulation therapy based on an individual's prior exposure to a pathogen.

BACKGROUND OF THE INVENTION

More than one in three people in the developed nations are diagnosed with cancer. More than one in four die from it. Therapies for cancer have primarily relied upon treatments such as surgery, chemotherapy, and radiation. These approaches however, while beneficial for some types and stages of cancer, have proved to be of limited efficacy in many common types and stages of cancers. For example, surgical treatment of a tumor requires complete removal of cancerous tissue to prevent reoccurrence. Similarly, radiation therapy requires complete destruction of cancerous cells. This is difficult since, in theory, a single malignant cell can proliferate sufficiently to cause reoccurrence of the cancer. Also, both surgical treatment and radiation therapy are directed to localized areas of cancer, and are relatively ineffective when the cancer metastasizes. Often surgery or radiation or both are used in combination with systemic approaches such as chemotherapy. Chemotherapy however has the problem of non-selectivity with the concomitant problem of deleterious side effects, as well as the possibility of the cancer cells developing resistance to the drugs.

The inherent shortcomings of chemotherapy have led to disparate efforts to recruit various aspects of the immune system to treat cancers. A subset of this work relates to immunization with microbial vaccines. Although this approach has a relatively long history, as discussed in more detail below, the field is a very confused mixture of sometimes intriguing successes mixed with many failures that together have failed to produce a cohesive therapeutic approach amenable to widespread clinical adoption.

Alternative approaches for the treatment of cancers have included therapies that involve augmentation of immune system function such as cytokine therapy (for e.g., recombinant interleukin 2 and gamma interferon for kidney cancers), dendritic cell therapy, autologous tumor vaccine therapy, genetically-altered vaccine therapy, lymphocyte therapy, and microbial vaccine therapies, the latter being thought to engage the host system in a non-specific manner. Microbial vaccines have been used to vaccinate subjects against pathogens that are associated with cancer, such as the human papillomavirus. Immunostimulatory microbial vaccines that are not targeted to cancer-causing organisms, i.e., non-specific immunostimulatory vaccines, such as pyrogenic vaccines, have a long clinical history that includes reports of successes and failures in treating a variety of cancers. For example, Coley's vaccine (a combination of Streptococcus pyogenes and Serratia marcescens) has been reported to be helpful for the treatment of sarcomas, and lymphomas (see, for e.g., Nauts H C, Fowler G A A, Bogato F H. A review of the influence of bacterial infection and of bacterial products [Coley's toxins] on malignant tumors in man. Acta Med Scand 1953; 145 [Suppl. 276]:5-103). Clinical trials have reportedly demonstrated the benefit of Coley's vaccine treatment for lymphoma and melanoma (see, for e.g., Kempin S, Cirrincone C, Myers J et al: Combined modality therapy of advanced nodular lymphomas: the role of nonspecific immunotherapy [MBV] as an important determinant of response and survival. Proc Am Soc Clin Oncol 1983; 24:56; Kolmel K F, Vehmeyer K. Treatment of advanced malignant melanoma by a pyrogenic bacterial lysate: a pilot study. Onkologie 1991; 14:411-17).

It has been suggested that the effectiveness of some non-specific bacterial cancer vaccines is attributable to particular bacterial components or products, such as bacterial DNA or endotoxin (LPS), or because they induce the expression of particular factors, such as tumor necrosis factor (TNF) or interleukin-12. A correspondingly broad range of physiological mechanisms have been ascribed to such treatments, ranging from generalized effects of fever to anti-angiogenic mechanisms. In accordance with these various principles, a wide variety of microbial vaccines have been tested as general immune stimulants for the treatment of cancer. While most have shown negative results, a few have shown some intriguing positive results in certain contexts, as discussed below.

Intradermal BCG (Mycobacterium bovis) vaccine treatment has been reported to be effective for the treatment of stomach cancer (see, for e.g., Ochiai T, Sato J, Hayashi R, et al: Postoperative adjuvant immunotherapy of gastric cancer with BCG-cell wall endoskeleton. Three- to six-year follow-up of a randomized clinical trial. Cancer Immunol Immunother 1983; 14:167-171) and colon cancer (Smith R E, Colangelo L, Wieand H S, Begovic M, Wolmark N. Randomized trial of adjuvant therapy in colon carcinoma: 10-Year results of NSABP protocol C-01. J. NCI 2004; 96[15]:1128-32; Uyl-de Groot C A, Vermorken J B, Hanna M G, Verboon P, Groot M T, Bonsel G J, Meijer C J, Pinedo H M. Immunotherapy with autologous tumor cell-BCG vaccine in patients with colon cancer: a prospective study of medical and economic benefits Vaccine 2005; 23[17-18]:2379-87).

Mycobacterium w vaccine therapy, in combination with chemotherapy and radiation, was found to significantly improve quality of life and response to treatment in patients with lung cancer (see for e.g., Sur P, Dastidar A. Role of Mycobacterium w as adjuvant treatment of lung cancer [non-small cell lung cancer]. J Indian Med Assoc 2003 February; 101[2]:118-120). Similarly, Mycobacterium vaccae vaccine therapy was found to improve quality of life (see, for e.g., O'Brien M, Anderson H, Kaukel E, et al. SRL172 [killed Mycobacterium vaccae] in addition to standard chemotherapy improves quality of life without affecting survival, in patients with advanced non-small-cell lung cancer: phase III results. Ann Oncol 2004 June; 15[6]; 906-14) and symptom control (Harper-Wynne C, Sumpter K, Ryan C, et al. Addition of SRL 172 to standard chemotherapy in small cell lung cancer [SCLC] improves symptom control. Lung Cancer 2005 February; 47[2]:289-90) in lung cancer patients.

Corynebacterium parvum vaccine was linked with a trend towards improved survival for the treatment of melanoma (see, for e.g., Balch C M, Smalley R V, Bartolucci A A, et al. A randomized prospective trial of adjuvant C. parvum immunotherapy in 260 patients with clinically localized melanoma [stage I]. Cancer 1982 Mar. 15; 49[6]:1079-84).

Intradermal Streptococcus pyogenes vaccine therapy was found to be effective for the treatment of stomach cancer (see, for e.g., Hanaue H, Kim D Y, Machimura T, et al. Hemolytic streptococcus preparation OK-432; beneficial adjuvant therapy in recurrent gastric carcinoma. Tokai J Exp Clin Med 1987 November; 12[4]:209-14).

Nocardia rubra vaccine was found to be effective for the treatment of lung cancer (see, for e.g., Yasumoto K, Yamamura Y. Randomized clinical trial of non-specific immunotherapy with cell-wall skeleton of Nocardia rubra. Biomed Pharmacother 1984; 38[1]:48-54; Ogura T. Immunotherapy of respectable lung cancer using Nocardia rubra cell wall skeleton. Gan To Kagaku Ryoho 1983 February; 10[2 Pt 2]:366-72) and linked to a trend to improved survival for the treatment acute myelogenous leukemia (Ohno R, Nakamura H, Kodera Y, et al. Randomized controlled study of chemoimmunotherapy of acute myelogenous leukemia [AML] in adults with Nocardia rubra cell-wall skeleton and irradiated allogeneic AML cells. Cancer 1986 Apr. 15; 57[8]:1483-8).

Lactobacillus casei vaccine treatment combined with radiation was found to more effective for the treatment of cervical cancer than radiation alone. (see, for e.g., Okawa T, Kita M, Arai T, et al. Phase II randomized clinical trial of LC9018 concurrently used with radiation in the treatment of carcinoma of the uterine cervix. Its effect on tumor reduction and histology. Cancer 1989 Nov. 1; 64[9]:1769-76)

Pseudomonas aeruginosa vaccine treatment was found to increase the effectiveness of chemotherapy in the treatment of lymphoma and lung cancer (see, for e.g., Li Z, Hao D, Zhang H, Ren L, et al. A clinical study on PA_MSHA vaccine used for adjuvant therapy of lymphoma and lung cancer. Hua Xi Yi Ke Da Xue Xue Bao 2000 September; 31 [3]:334-7).

Childhood vaccination with the smallpox vaccine (i.e., Vaccinia virus vaccine) was found to be associated with a decreased risk of melanoma later in life (see, for e.g., Pfahlberg A, Kolmel K F, Grange J M. et al. Inverse association between melanoma and previous vaccinations against tuberculosis and smallpox: results of the FEBIM study. J Invest Dermatol 2002[119]:570-575) as well as decreased mortality in those patients who did develop melanoma (see, for e.g., Kolmel K F, Grange J M, Krone B, et al. Prior immunization of patients with malignant melanoma with vaccinia or BCG is associated with better survival. European Organization for Research and Treatment of Cancer cohort study on 542 patients. Eur J Cancer 41[2005]:118-125).

Treatment with rabies virus vaccine was found to result in temporary remission in 8 of 30 patients with melanoma (see, for e.g., Higgins G, Pack G. Virus therapy in the treatment of tumors. Bull Hosp Joint Dis 1951; 12:379-382; Pack G. Note on the experimental use of rabies vaccine for melanomatosis. Arch Dermatol 1950; 62:694-695).

In spite of substantial efforts to engage the immune system to combat cancers using non-specific immunostimulatory microbial vaccines, the vast majority of these efforts have failed and there is little clinical or research evidence of widespread success in improving the survival of cancer patient populations. While it has been recognized that immunostimulatory microbial vaccine approaches have promise, it has also been recognized that significant challenges characterize the field (see, for e.g., Ralf Kleef, Mary Ann Richardson, Nancy Russell, Cristina Ramirez. “Endotoxin and Exotoxin Induced Tumor Regression with Special Reference to Coley Toxins: A Survey of the Literature and Possible Immunological Mechanisms.” Report to the National Cancer Institute Office of Alternative and Complementary Medicine August 1997; DL Mager. “Bacteria and Cancer: Cause, Coincidence or Cure? A Review.” Journal of Translational Medicine 28 Mar. 2006 4[14]:doi:10.1186/1479-5876-4-14).

In addition to treating cancers, immunomodulatory therapies have also been used in the treatment of a wide variety of conditions characterized by inflammation. For example, inflammatory bowel disease (IBD) is a name frequently given to a group of inflammatory conditions of the colon and small intestine, generally characterized by similar symptoms and indeterminate etiology. Major sub-types of IBD are recognized clinically as Crohn's disease and ulcerative colitis. In addition to Crohn's disease and ulcerative colitis, IBD may also include conditions recognized as any one of the following: collagenous colitis, lymphocytic colitis, ischaemic colitis, diversion colitis, Behçet's syndrome or indeterminate colitis. The difference between these conditions relate primarily to the location and nature of the inflammatory changes in the gastrointestinal tract (GIT). Crohn's disease, for example, is generally recognized as potentially affecting any part of the gastrointestinal tract, from mouth to anus, with a majority of the cases marked by relapsing and remitting granulomatous inflammation of the alimentary tract in the terminal ileum and colon. Ulcerative colitis, in contrast, is generally considered to be restricted to the colon and the rectum. The various regions of the gastrointestinal tract in which these inflammatory conditions may exhibit symptoms include: the bowel or intestine, including: the small intestine (which has three parts: the duodenum, the jejunum, and the ileum); the large intestine (which has three parts: the cecum, the colon, which includes the ascending colon, transverse colon, descending colon and sigmoid flexure; and the rectum); and, the anus.

The understanding of inflammatory bowel diseases is evolving, but is as yet incomplete in many respects (see, for e.g., Baumgart D C, Carding S R (2007) “Inflammatory bowel disease: cause and immunobiology” The Lancet 369 (9573): 1627-40; Baumgart D C, Sandborn W J (2007) “Inflammatory bowel disease: clinical aspects and established and evolving therapies” The Lancet 369 (9573): 1641-57; Xavier R J, Podolsky D K (2007) “Unravelling the pathogenesis of inflammatory bowel disease” Nature 448 (7152): 427-34; J. H. Cho (2008) “The genetics and immunopathogenesis of inflammatory bowel disease” Nature Reviews Immunology 8, 458-466).

Anti-inflammatory drugs and immune system suppressants may be used in the treatment of IBD, such as sulfasalazine (Azulfidine™), mesalamine (Asacol™, Rowasa™), corticosteroids (e.g. prednisone), azathioprine (Imuran™), mercaptopurine (Purinethol™), infliximab (Remicade™) adalimumab (Humira™), certolizumab pegol (Cimzia™), methotrexate (Rheumatrex™), cyclosporine (Gengraf™, Neoral™, Sandimmune™) or natalizumab (Tysabri™).

Alternative treatments for IBD have been suggested, including the use of various biological agents, or treatments that purportedly adjust natural intestinal flora, sometimes called probiotic treatments (US 2007/0258953; US 2008/0003207; WO 2007/076534; WO 2007/136719; WO 2010/099824). It has for example been reported that IBD may be treated with a deliberate infestation of parasitic worms, for example by consumption of the live ova of the Trichuris suis helminth (Summers et al. (2003) “Trichuris suis seems to be safe and possibly effective in the treatment of inflammatory bowel disease”. Am. J. Gastroenterol. 98 (9): 2034-41; Büning et al., (2008) “Helminths as governors of inflammatory bowel disease” Gut 57:1182-1183; Weinstock and Elliott (2009) “Helminths and the IBD hygiene hypothesis” Inflamm Bowel Dis. 2009 January; 15(1):128-33).

IBD is representative of a long list of conditions that are characterized by pathological inflammation, for which symptomatic treatment with anti-inflammatory medications is a common approach, often in the absence of a clear understanding of the etiology of the disease. Many of these inflammatory diseases, such as IBD and arthritis, are very common, but remain difficult to treat.

SUMMARY OF THE INVENTION

In one aspect, the invention provides methods and compositions for treating an individual for a condition characterized by inflammation or disease in a specific organ or tissue. The methods may involve determining whether the individual has previously been infected with at least one pathogen that is pathogenic in the specific organ or tissue; and administering to the individual a therapeutic composition comprising antigenic determinants, the antigenic determinants selected or formulated so that together they are specific for the at least one pathogen.

In another aspect, the invention provides methods of formulating compositions of the invention for treating an individual for a condition characterized by disease or inflammation in a specific organ or tissue. The methods may involve determining whether the individual has previously been infected with at least one pathogen that is pathogenic in the specific organ or tissue; producing an antigenic composition comprising antigenic determinants that together are specific for the at least one pathogen; and formulating the antigenic composition for administration as a therapeutic or anti-inflammatory composition capable of eliciting an immunological or anti-inflammatory response in the specific organ or tissue.

The methods detailed herein may involve identifying the presence of at least one antibody that recognizes the at least one pathogen. The methods may also or alternatively involve identifying at least one memory B cell that recognizes the at least one pathogen. The methods may also or alternatively involve identifying at least one memory T cell that recognizes the at least one pathogen. The methods may for example involve obtaining the antibody, the memory B cell, or the memory T cell from peripheral circulation or from the targeted specific organ or tissue of the individual.

In another aspect, the invention provides methods of treating an individual for a condition or disease or inflammation in a specific organ or tissue. The method may involve administering to the individual an infectious dose of at least one pathogen that is pathogenic in the specific organ or tissue, such as an attenuated pathogen; and administering to the individual an anti-inflammatory composition comprising antigenic determinants, the antigenic determinants selected or formulated so that together they are specific for the at least one pathogen, such as a composition comprising killed whole pathogens. The method may involve these two administration steps occurring simultaneously. The method may involve the second step occurring between 1 hour and 30 days after the first step.

Diseases or conditions that may be treated in accordance with alternative aspects of the invention includes cancers characterized by the presence of a tumour in the specific organ or tissue of the individual. Alternative diseases or conditions include autoimmune diseases characterized by an immune reaction in the specific organ or tissue that is targeted for treatment, such as arthritis or IBD.

Compositions of the invention may for example be formulated or used for administration at a site that is distinct from the specific organ or tissue that is targeted for treatment, for example by subcutaneous injection or intradermal injection. Compositions may for example be formulated for repeated administration, for example by subcutaneous or intradermal injection. In selected embodiments, compositions of the invention may be formulated or used so as to produce a localized immune response at a site of administration, for example at a site of injection in the skin.

In selected embodiments, pathogens may be selected for use in methods and compositions of the invention on the basis that the pathogen is endogenous to the specific organ or tissue that is targeted for treatment. Alternatively, the pathogen may be exogenous to the specific organ or tissue. The pathogen may be formulated as an attenuated or a killed pathogen, for example to provide anantigenic composition of whole attenuated or killed pathogens. For example, the pathogen may be a bacterium, a virus, a protozoa, a fungus, or a helminth.

In a further aspect, a method of formulating an anti-inflammatory composition for treating a condition characterized by inflammation in a specific organ or tissue is provided. The method involves selecting at least one pathogen that is pathogenic in the specific organ or tissue; producing an antigenic composition comprising antigenic determinants that together are specific for the pathogen; and formulating the antigenic composition for administration as an anti-inflammatory composition capable of eliciting an anti-inflammatory response in the specific organ or tissue, for example wherein the condition characterized by inflammation is not a cancer, for example wherein the condition is IBD or arthritis.

The method may further involve a diagnostic step of identifying the specific organ or tissue within which the inflammation is symptomatic prior to producing the antigenic composition. Optionally, a tumor or proliferative condition may be situated in the specific organ or tissue.

Optionally, the antigenic composition may be formulated for subcutaneous injection or intradermal injection. Optionally, the antigenic composition may be formulated for injection to produce a localized skin immune response at a site of administration. Optionally, the method detailed herein is provided such that when a specific tissue or organ is determined, the pathogen is selected from a particular group of pathogens as described herein. In one aspect the pathogen is one that is an endogenous organism, which is a natural cause of infection in the tissue or organ in question. Optionally, the pathogen is an exogenous organism that is a natural cause of infection in the tissue or organ is question, and may include, for example, a bacteria, virus, helminth, or fungus.

Optionally, the antigenic composition may be formulated for repeated subcutaneous or intradermal administration. Optionally, the antigenic composition may be formulated for administration by a route that is not enteric. Optionally, the pathogen detailed herein is a bacteria, a virus, a protozoa, a fungus or a helminth. Further, the method may involve killing or attenuating the pathogen to formulate the antigenic composition as a whole killed or attenuated pathogen composition. The pathogen may be a member of a species of the endogenous flora that is a natural cause of infection in the specific organ or tissue. The pathogen may be an exogenous species that is a natural cause of infection in the specific organ or tissue.

In another aspect, a method of treating an individual for a condition characterized by inflammation in a specific organ or tissue is provided. The method involves administering to the individual an anti-inflammatory composition comprising antigenic determinants. The antigenic determinants are selected or formulated so that together they are specific for at least one pathogen that is pathogenic in the specific organ or tissue. Optionally, the anti-inflammatory composition may be administered at an administration site in successive doses given at a dosage interval of between one hour and one month, over a dosage duration of at least two weeks. Further, and without limitation, the dosing may comprise two or more doses over a period from four (4) days to one (1) week.

In another aspect, use of an anti-inflammatory composition for treating an individual for a condition characterized by inflammation in a specific organ or tissue is disclosed. The anti-inflammatory composition contains antigenic determinants selected or formulated so that together they are specific for at least one microbial pathogen that is pathogenic in the specific organ or tissue.

In another aspect, use of an anti-inflammatory composition to formulate a medicament for treating an individual for a condition characterized by inflammation in a specific organ or tissue is disclosed. The anti-inflammatory composition contains antigenic determinants selected or formulated so that together they are specific for at least one microbial pathogen that is pathogenic in the specific organ or tissue.

Optionally, the uses disclosed herein include those in which the individual has a cancer situated in the organ or tissue. Further, and optionally, the anti-inflammatory composition may be administered at an administration site in successive doses given at a dosage interval of between one hour and one month, over a duration of at least two weeks. Further, and without limitation, the dosing may comprise two or more doses over a period from four (4) days to one (1) week.

In one aspect, a method of comparing immune responses is provided. The method involves administering to an animal having an organ or tissue a medicament having an antigenic composition having antigenic determinants selected or formulated so that together the antigenic determinants are specific for at least one microbial pathogen that is pathogenic in the organ or tissue, extracting a quantifiable immune sample from the organ or tissue, measuring a characteristic of the immune response in the organ or tissue in the quantifiable immune sample following the administration of the medicament, and, comparing the characteristic of the immune response in the quantifiable immune sample to a corresponding characteristic of the immune response in a reference immune sample obtained from a corresponding organ or tissue. Optionally, the reference immune sample may be obtained from the corresponding organ or tissue in the animal prior to the step of administering the medicament. Optionally, the reference immune sample may be obtained from the corresponding organ or tissue in a second animal. Optionally, the animal may have a cancer situated in the organ or tissue.

Comparing the characteristic of the immune response may involve comparing, in the quantifiable and reference immune samples, an indication of the numbers of any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Further, comparing the characteristic of the immune response may involve comparing a shift in an activation state of macrophages. Optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. Further and optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cellular markers on any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages.

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cytokines produced by any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. As detailed herein, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, the cytokines are produced as a result of a shift in an activation state of the macrophages. Optionally, the macrophages shift from being M2-like macrophages to being M1-like macrophages. Further and optionally, the macrophages shift from being M1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, differential gene expression produced by any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, the differential gene expression is produced as a result of a shift in an activation state of the macrophages. Optionally, macrophages may shift from being M2-like macrophages to being M1-like macrophages. Further and optionally, the macrophages shift from being M1-like macrophages to being M2-like macrophages.

Optionally, the medicament may be administered at an administration site in successive doses given at a dosage interval of between one hour and one month, over a dosage duration of at least one week. Optionally, the medicament may be administered intradermally or subcutaneously. Optionally, the medicament may be administered in a dose so that each dose is effective to cause a visible localized inflammatory immune response at the administration site. Optionally, the medicament may be administered so that visible localized inflammation at the administration site occurs within 1 to 48 hours. Further and optionally, the animal may be a mammal. Optionally, the animal may be a human or a mouse.

In another aspect, a method of selecting a therapeutic preparation suitable for treating an individual for a cancer in a specific organ or tissue is provided. The method involves providing an animal having a cancer situated in a specific organ or tissue, providing a test preparation having one or more antigenic determinants of a microbial pathogen which is pathogenic in the corresponding specific organ or tissue in a healthy individual, measuring a characteristic of the immune response in a reference immune sample obtained from the organ or tissue of the animal, administering the test preparation to the animal, measuring a characteristic of the immune response in a quantifiable immune sample obtained from a corresponding organ or tissue of the animal, comparing the characteristic of the immune response in the in the reference and quantifiable immune samples, and treating an enhanced characteristic of the immune response in the quantifiable immune sample compared to the reference immune sample as an indication of the suitability of the test preparation as a therapeutic preparation. Optionally, the animal is sacrificed before the quantifiable immune sample has been obtained.

Optionally, comparing the characteristic of the immune response may involve comparing, in the quantifiable and reference immune samples, an indication of the numbers of any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, comparing the characteristic of the immune response may involve comparing a shift in an activation state of macrophages. Optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. Further and optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cellular markers on any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages.

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cytokines produced by any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, the cytokines are produced as a result of a shift in an activate state of the macrophages. Optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. Further, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

Further and optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, differential gene expression produced by any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, the differential gene expression may be produced as a result of a shift in an activation state of the macrophages. Optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. Further and optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

In another aspect, a method of selectively targeting an immune response to a cancerous tissue or an organ in a human subject is provided. The method involves administering to the subject a medicament having an effective amount of a microbial pathogen antigenic composition, wherein the microbial pathogen may be pathogenic in the specific cancerous organ or tissue of the subject and the antigenic composition comprises antigenic determinants that together are specific for the microbial pathogen. Optionally, the antigenic composition may include a whole killed bacterial cell composition. Optionally, the medicament may be administered to the subject in an amount and for a time that is effective to up-regulate an immune response in the cancerous organ or tissue of the subject. Optionally, the method may further involve measuring a characteristic of the immune response. The method also includes treatment of pre-cancerous lesions including, but not limited to, actinic keratosis, cervical dysplasia, and colonic adenomas.

In another aspect, a method for treating a human subject for a cancer situated in a tissue or an organ is provided. The method involves administering to the subject a medicament having an effective amount of a microbial pathogen antigenic composition comprising a whole killed bacterial cell composition, wherein the microbial pathogen is pathogenic in the specific organ or tissue of the subject within which the cancer is situated. The medicament may be administered to the subject in an amount and for a time that is effective to modulate an immune response. Optionally, the modulation of the immune response may involve a shift in the activation state of macrophages. Optionally, the modulation of the immune response may involve shifting from a M2-like macrophage response to a M1-like macrophage response. The modulation of the immune response may involve a shift from M1-like macrophages to M2-like macrophages, as those terms are defined herein. Optionally and without limitation, the method may further involve measuring a characteristic of the immune response.

Optionally, comparing the characteristic of the immune response may involve comparing, in the quantifiable and reference immune samples, an indication of the numbers of any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, comparing the characteristic of the immune response may involve comparing a shift in an activation state of macrophages. Further and optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. Optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

Further and without limitation, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cellular markers on any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cytokines produced by any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Further, cytokines may be produced as a result of a shift in an activation state of the macrophages. The macrophages may shift from being M2-like macrophages to being M1-like macrophages. Optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

Further and optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, differential gene expression produced by any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, the differential gene expression may be produced as a result of a shift in an activation state of the macrophages. Further and optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. The macrophages may shift from being M1-like macrophages to being M2-like macrophages.

In another aspect, a method of monitoring efficacy of a treatment regime in an individual being treated for a cancer in a specific organ or tissue is provided. The method involves measuring a characteristic of an immune response in a post-treatment immune sample obtained from the specific organ or tissue after the individual has been subject to the treatment regime for a period of time, wherein the presence of a characteristic of the immune response which is greater in magnitude than would be expected had the individual not been subject to the treatment regime, is indicative of the efficacy of the treatment regime; and the treatment regime involves administering a preparation comprising one or more antigenic determinants of a microbial pathogen which is pathogenic in the corresponding specific organ or tissue in a healthy subject.

The method detailed herein may further involve measuring the characteristic of the immune response in a pre-treatment reference sample, wherein the pre-treatment reference sample was obtained from the specific organ or tissue before, at the same time as or after commencement of the treatment regime, but prior to obtaining the post-treatment immune sample, and comparing the characteristic of the immune response in the pre-treatment and post-treatment samples, wherein an increase in the magnitude of the immune response in the post-treatment immune sample compared to the pre-treatment reference sample is indicative of the efficacy of the treatment regime. Optionally, measuring the characteristic of the immune response may involve determining an indication of the number of inflammatory monocytes in a sample of the organ or tissue. Optionally, measuring the characteristic of the immune response may involve determining an indication of the number of macrophages in a sample of the organ or tissue. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages.

As detailed herein in another aspect, the invention also provides methods for formulating an immunogenic composition for treating a cancer situated in a specific organ or tissue in a mammal, such as human patient. The method may include selecting at least one microbial pathogen that is naturally pathogenic in the organ or tissue of the mammal within which the cancer is situated. An antigenic composition may be produced that includes antigenic determinants that together are specific for or characteristic of the microbial pathogen.

A diagnostic step may be used to identify the specific organ or tissue within which the cancer is situated, prior to producing the antigenic composition targeted to the site of the cancer. The site of the cancer may be a primary site, or a secondary site of metastasis. The antigenic composition may be sufficiently specific that it would be capable of eliciting an immune response in the mammal specific to the microbial pathogen. The antigenic composition may be a bacterial composition, for example derived from a bacterial species or species that are endogenous to the flora of the patient or from an exogenous species or species. In alternative embodiments, the antigenic composition may be derived from a virus or viruses. Accordingly, the microbial pathogen from which the antigenic composition is derived may be a virus. The microbial pathogen may be killed. In alternative embodiments, the microbial pathogen may be live or attenuated. Immunogenic compositions of the invention may also be formulated or administered with anti-inflammatory modalities, such as an NSAID. The site of administration may be at a site distant from the site of the cancer, for example in an organ or tissue that is not the organ or tissue within which the cancer is situated, for example the skin or subcutaneous tissue.

The antigenic composition may for example be formulated for subcutaneous injection, intradermal injection or oral administration. In embodiments for subcutaneous or intradermal injection, the dosing or formulation of the antigenic composition may be adjusted in order to produce a localized immune reaction visible in the skin at the site of administration, for example an area of inflammation from 2 mm to 100 mm in diameter appearing, for example, 2-48 hours after administration and lasting, for example, 2-72 hours or longer. The antigenic composition may be formulated for repeated subcutaneous or intradermal administration, for example at alternating successive sites.

In some embodiments, the invention involves methods of treating a mammal for a cancer situated in a tissue or an organ. In alternative embodiments, the treatment may anticipate the development of the cancer in the tissue, for example if the site of a primary tumour suggests the likelihood of metastasis to a particular tissue or organ, then the patient may be prophylactically treated to prevent or ameliorate metastasis to that tissue or organ. The method may include administering to the subject an effective amount of an antigenic composition comprising antigenic determinants that together are specific for at least one microbial pathogen. An aspect of the invention involves the use of a microbial pathogen that is pathogenic in the specific organ or tissue of the mammal within which the cancer is situated. The antigenic composition may be administered, for example by subcutaneous or intradermal injection at an administration site, in successive doses given at a dosage interval, for example of between one hour and one month, over a dosage duration, for example of at least 1 week, 2 weeks, 2 months, 6 months, 1, 2, 3, 4, or 5 years or longer. Each injection dose may for example be metered so that it is effective to cause visible localized inflammation at the administration site, appearing, for example, 1-48 hours after injection.

In another aspect, methods are provided for treating cancers of a specific organ or tissue in a subject by administering one or more antigens of one or more microbial pathogens, such as bacterial, viral or fungal species that are pathogenic in the specific organ or tissue.

In alternative embodiments, the pathogenic microbial species may be capable of causing infection naturally, (i.e., without human intervention) in the specific organ or tissue in a healthy subject, or may have caused an infection in the specific organ or tissue in a healthy subject. In alternative embodiments, the antigen may be administered by administering preparations derived from whole cells of a microbial species. In alternative embodiments, the method may, for example, include administering at least two or more microbial species, or administering at least three or more microbial species, and the microbes may be bacteria or viruses. In alternative embodiments, the method may further include administering a supplement or an adjuvant. An aspect of the invention involves administering antigenic compositions so as to elicit an immune response in said subject.

In alternative embodiments, the microbial pathogen in the antigenic composition may be killed, and thus rendered non-infectious. In some embodiments, the antigenic composition is administered at a site distant from the cancer site, and in selected embodiments of this kind, methods of the invention may be carried out so that they do not produce infection at the cancer site.

As detailed herein, various aspects of the invention involve treating cancers. In this context, treatment may be carried out so as to provide a variety of outcomes. For example, treatment may: provoke an immune reaction that is effective to inhibit or ameliorate the growth or proliferation of a cancer; inhibit the growth or proliferation of cancer cells or tumors; cause remission of a cancer; improve quality of life; reduce the risk of recurrence of a cancer; inhibit metastasis of a cancer; or, improve patient survival rates in a patient population. In this context, extending the life expectancy of a patient, or patient population, means to increase the number of patients who survive for a given period of time following a particular diagnosis. In some embodiments, treatment may be of patients who have not responded to other treatments, such as patients for whom a chemotherapy or surgery has not been an effective treatment. Treatment in alternative embodiments may for example be before or after onset of cancer. For example prophylactic treatment may be undertaken, for example of patients diagnosed as being at risk of a particular cancer. For example a patient having a genetic or lifestyle predisposition to cancer of a certain tissue or organ may be treated with an immunogenic composition comprising antigenic determinants of a pathogen that is pathogenic in that organ or tissue. Similarly, the prophylactic treatment of metastasis may be undertaken, so that patients having a primary cancer with a propensity to metastasize to a particular tissue or organ may be treated with an immunogenic composition comprising antigenic determinants of a pathogen that is pathogenic in that organ or tissue.

In another aspect, a method of treating a cancer situated in a lung in a subject is provided. The method involves administering to the subject an effective amount of an antigen of one or more microbial species that is pathogenic in the lung and administering to the subject an effective amount of a platinum-containing chemotherapeutic agent. The microbial species may be a viral pathogen or a bacterial pathogen or a fungal pathogen. Further, the microbial species may be an endogenous species or an exogenous species.

In another aspect, use of an effective amount of an antigen of one or more microbial species that is pathogenic in the lung is provided to formulate a medicament for use with a platinum-containing chemotherapeutic agent for treating lung cancer in a subject. In another aspect, use of an effective amount of an antigen of one or more microbial species that is pathogenic in the lung is provided for use with a platinum-containing chemotherapeutic agent for treating lung cancer in a subject. The microbial species may be a viral pathogen or a bacterial pathogen or a fungal pathogen. Further, the microbial species may be an endogenous species or an exogenous species.

In another aspect, a kit is provided. The kit includes an antigen of one or more microbial species that is pathogenic in the lung, a platinum-containing chemotherapeutic agent; and instructions for providing the antigen and the platinum-containing chemotherapeutic agent to a subject in need thereof. The microbial species may be an endogenous bacterial pathogen. It may also be an exogenous pathogen and may, for example, be a viral pathogen or an exogenous bacterial pathogen or a fungal pathogen.

In various aspects, the invention provides methods for treating inflammatory conditions or immune diseases. For example, the invention provides methods for formulating and using an immunogenic composition for treating an IBD or arthritis or another disease associated with an inflammatory condition. The IBD may for example be an IBD that is symptomatic in one or more regions of the GIT of a human patient, such as Crohn's disease, ulcerative colitis, collagenous colitis, lymphocytic colitis, ischaemic colitis, diversion colitis, Behçet's syndrome or indeterminate colitis. The treatment of the patient may involve a diagnostic step of identifying the region of the GIT within which the IBD is symptomatic. The formulation may comprise an antigenic composition comprising antigenic determinants that together are specific for at least one pathogen, such as a bacteria, a virus, a protozoa or a helminth, or a fungus that is pathogenic in the effected region of the GIT. The formulation may be prepared for administration as an immunogenic composition capable of eliciting an immune reaction to treat the IBD. The composition may for example be formulated for a route that is not enteric, such as subcutaneous injection or intradermal injection, for example to produce a localized skin immune response, such as an inflammatory response, at a site of administration. The pathogen for treating immune diseases may be an endogenous organism, which is a natural cause of infection in the organ or tissue in question. The pathogen may be an exogenous organism, which is a natural cause of infection in the tissue or organ in question, and may include, for example, a bacteria, virus, helminth, or fungus.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a survival curve for a cumulative series of patients diagnosed with stage 3B or 4 inoperable lung cancer (all patients), comparing patients treated with MRV, patients not treated with the MRV, and a standard SEER survival curve.

FIG. 2 shows a survival curve for a cumulative series of patients diagnosed with stage 3B or 4 inoperable lung cancer (patients treated for at least 2 months with MRV), comparing patients treated with MRV, patients not treated with the MRV, and a standard SEER survival curve.

FIG. 3 shows a survival curve for a cumulative series of patients diagnosed with stage 3B or 4 lung cancer, illustrating the benefits of treatment with the MRV composition of the invention, comparing patients treated with MRV, patients not treated with the MRV, and a standard SEER survival curve.

FIG. 4 shows a survival curve for a cumulative series of patients diagnosed with stage 3B or 4 lung cancer, illustrating the effect of treatments for at least 2 months, comparing patients treated with MRV, patients not treated with the MRV, and a standard SEER survival curve.

FIG. 5 shows a survival curve for a cumulative series of patients diagnosed with stage 3B or 4 lung cancer, illustrating the effect of treatments for at least 6 months duration, comparing patients treated with MRV, patients not treated with the MRV, and a standard SEER survival curve.

FIG. 6 shows a survival curve for a cumulative series of 52 breast cancer patients with metastases to bone and/or lung, comparing patients treated with MRV, patients not treated with the MRV, and a standard SEER survival curve.

FIG. 7 is a comparison of survival of a cumulative series of metastatic prostate cancer patients who had surgery or radiation to destroy their prostate gland (and thus, the primary tumour) and who had detectable cancer limited to bone metastases, comparing patients treated with MRV, patients not treated with the MRV, and a standard SEER survival curve.

FIG. 8 shows a survival curve for a cumulative series of patients initially diagnosed with Stage 4 colorectal cancer, comparing patients treated with PVF, patients treated with MRV, patients not treated with an antigenic composition and a standard SEER survival curve.

FIG. 9 shows a survival curve for a cumulative series of patients initially diagnosed with Stage 4 Colorectal Cancer, with date from patients receiving treatment within 3 months of diagnosis, comparing patients treated with PVF, patients treated with MRV, patients not treated with an antigenic composition and a standard SEER survival curve.

FIG. 10 shows a survival curve for a cumulative series of stage 3B lung cancer patients who were treated with an oral antigen therapy, Respivax, compared to patients who did not use an antigenic composition.

FIG. 11 shows a survival curve for a cumulative series of patients diagnosed with stage 3B lung cancer, illustrating the benefits of treatment with the MRV composition of the invention, comparing patients treated with MRV, patients not treated with the MRV, and a standard SEER survival curve.

FIG. 12 shows a survival curve measured from date of first visit for a cumulative series of patients diagnosed with stage 3B lung cancer, illustrating the benefits of treatment with the MRV composition of the invention, comparing patients treated with MRV, patients not treated with the MRV, and a standard SEER survival curve.

FIG. 13 shows a survival curve for a cumulative series of patients diagnosed with stage 3B lung cancer whose first visit was within 3 months of diagnosis, illustrating the benefits of early treatment with the MRV composition of the invention, comparing patients treated with MRV and patients not treated with the MRV.

FIG. 14 shows a photograph of lungs from mice treated (row 1) and not-treated (row 2) with K. pneumoniae cells-only vaccine following challenge with Lewis lung carcinoma cells, as described in Example 4A herein. The bottom row (not-numbered) depicts lungs from mice that were not exposed to the mouse model of lung cancer.

FIG. 15 shows the average tumor volume of mice treated [AB1-AB6] and not-treated [AB-7] with bacterial vaccines following challenge with B16 melanoma cells, as described in Example 4B herein.

FIG. 16 shows a survival curve of colon cancer model mouse groups treated with or without a variety of bacterial vaccines, as described in Example 4C herein.

FIG. 17 shows the number of inflammatory monocytes and dendritic cells in the draining lymph node, lungs, and spleen following treatment with either a K. pneumoniae antigenic composition or PBS, as described in Example 5A herein.

FIG. 18 shows the total number of monocytes and dendritic cells in the lung, peritoneum and spleen of mice following treatment with either a K. pneumoniae antigenic composition, an E. coli antigenic composition, or PBS, as described in Example 5B herein.

FIG. 19 shows the total number of CD4+ T cells, CD8+ T cells, and NK cells from mice treated with either a K. pneumoniae antigenic composition, an E. coli antigenic composition, or PBS, as described in Example 5B herein.

FIG. 20 shows the total number of (A) inflammatory monocytes and (B) CD4+ T cells, CD8+ T cells, and NK cells on either of day 9 or 16 from mice treated with either heat-inactivated a K. pneumoniae antigenic composition, a phenol-inactivated K. pneumoniae antigenic composition, or PBS, as described in Example 5C herein.

FIG. 21 shows the total number of (A) inflammatory monocytes and dendritic cells and (B) CD4+ T cells, CD8+ T cells, and NK cells from mice treated with either a heat-inactivated K. pneumoniae antigenic composition, a phenol-inactivated K. pneumoniae antigenic composition, or PBS, as described in Example 5D herein.

FIG. 22 shows the total number of tumour nodules in mice treated with either PBS, or different dosages of K. pneumoniae antigenic composition as described herein.

FIG. 23 shows a photograph of lungs from mice treated with either PBS, or different dosages of K. pneumoniae antigenic composition as described herein.

FIG. 24 shows the total number of tumour nodules in mice treated with either PBS, or different dosages of K. pneumoniae antigenic composition as described herein.

FIG. 25 shows the total number of tumour nodules in mice treated with either PBS, or dosages of K. pneumoniae antigenic composition in combination (or not) with cisplatin as described herein.

FIG. 26 shows a survival curve for mice injected with Lewis Lung carcinoma cells and treated with either (i) vehicle control; (ii) Cisplatin; (iii) antigenic composition or (iv) antigenic composition and Cisplatin.

FIG. 27 shows the percentage of CD11b+ myeloid cells in the blood on day 13 of the relevant experiment detailed herein.

FIG. 28 shows (left panel) the frequency of CD11b+ NK1.1− cells from lungs of mice treated with various dosages of K. pneumoniae antigenic compositions or with PBS control or (right panel) the frequency of CD11b+ NK1.1+ cells from lungs of mice treated with various dosages of K. pneumoniae antigenic compositions or with PBS control.

FIG. 29 shows the amounts of numerous cytokines detected (in pg/g) from lung tissue derived from mice treated with various dosages of K. pneumoniae antigenic compositions or with PBS control.

FIG. 30 shows the amounts of numerous cytokines detected (in pg/ml) from BAL fluid from mice treated with various dosages of K. pneumoniae antigenic compositions or with PBS control.

FIG. 31 shows the relative gene expression ratios of NOS2 to Arg1 from mice treated with various dosages of K. pneumoniae antigenic compositions or with PBS control.

FIG. 32 shows the relative frequency of CD206 expression in lung macrophages from mice treated with various dosages of K. pneumoniae antigenic compositions or with PBS control.

FIG. 33 shows the relative frequency of F4/80 expression in lung macrophages from mice treated with various dosages of K. pneumoniae antigenic compositions or with PBS control.

FIG. 34 shows the relative frequency of CD11b+ Gr-1+ cells detected from the colons of mice treated with either K. pneumoniae or E. coli antigenic compositions or with PBS control.

FIG. 35 shows the relative frequency of CD11b+ Gr-1+ cells detected from the lungs of mice treated with either K. pneumoniae or E. coli antigenic compositions or with PBS control.

FIG. 36 shows the relative frequency of CD11b+ cells that were M1-like as isolated from subQ 4T1 tumours (left panel) and the relative frequency of CD11b+ cells that were M2-like as isolated from subQ 4T1 tumours (right panel).

FIG. 37 shows the tumour volume (mm³) from mice treated with either indomethacin and PBS; or indomethacin and a S. aureus antigenic composition; or EtOH and PBS; or EtOH and a S. aureus antigenic composition [left panel]. The right panel of this Figure also shows the relative frequency and makeup of CD11b+ cells in the tumours at day 11 of the relevant experiment detailed herein.

FIG. 38 shows the relative frequency and makeup of CD11b+ cells in the tumours at day 22 of the relevant experiment detailed herein.

FIG. 39 shows the tumour volume in cohorts of animals treated with Indomethacin, Indomethacin+antigenic compositions, vehicle alone, or antigenic compositions alone.

FIG. 40 shows the percentage of CD11b+ cells in the tumours of animals treated with Indomethacin, Indomethacin+antigenic compositions, vehicle alone, or antigenic compositions alone (Day 11 data).

FIG. 41 shows the percentage of CD11b+ cells in the tumours of animals treated with Indomethacin, Indomethacin+antigenic compositions, vehicle alone, or antigenic compositions alone (Day 22 data).

FIG. 42 shows the percentage of CD11b+ CD94+ cells in the tumours of animals treated with Indomethacin, Indomethacin+antigenic compositions, vehicle alone, or antigenic compositions alone (Day 22 data).

FIG. 43 shows the relative expression of (A) Fizz1 and (B) Ym1 in excised tumors as described herein.

FIG. 44 shows the relative expression of (A) Arg1 and (B) Fizz1 from tumors and spleens [(C) and (D)] as described herein.

FIG. 45 shows the relative expression of Nos2 and Ym1 from tumors and spleens as described herein.

FIG. 46 shows the amount of IFN-γ produced in the lungs of mice with and without tumours and with and without antigenic composition treatment as described herein.

FIG. 47 shows the amount of IL-10 produced from bone marrow macrophages cultured overnight with K. pneumoniae antigenic composition, LPS, and media alone.

FIG. 48 shows the relative expression of IL-10 produced in the tumours of mice under conditions described herein.

FIG. 49 shows a percentage of weight change in C57BL/6 mice treated with and without antigenic compositions derived from E. coli in a DSS-induced colitis mouse model.

FIG. 50 shows the levels of IL-17 present in colons from C57BL/6 mice treated with and without antigenic compositions derived from E. coli in a DSS-induced colitis mouse model.

FIG. 51 shows the clinical score of mice treated with and without antigenic compositions derived from E. coli in a DSS-induced colitis mouse model.

FIG. 52 shows the weight change in mice treated with and without antigenic compositions derived from E. coli in a DSS-induced colitis mouse model.

FIG. 53 shows the anti-tumour efficacy of antigenic compositions derived from S. pneumoniae is determined by previous exposure to live S. pneumoniae. The top panel depicts the percent survival of mice treated with and without antigenic compositions derived from S. pneumoniae where there was no previous exposure to S. pneumoniae. The middle panel depicts the percent survival of mice treated with and without antigenic compositions derived from S. pneumoniae where there was either no prior exposure to S. pneumoniae or there was current colonization by S. pneumoniae. The bottom panel depicts the percent survival of mice treated with and without antigenic compositions derived from S. pneumoniae where there was either no prior exposure to S. pneumoniae or there was past exposure to S. pneumoniae.

DETAILED DESCRIPTION OF THE INVENTION

In various aspects, the invention relates to the surprising discovery that administration of formulations that include antigenic determinants of microbial pathogens that are pathogenic in a particular tissue or organ, is effective in treating inflammation or cancer situated in that specific tissue or organ. Compositions of the invention may for example be administered at a site that is distant from the site of inflammation or cancer. Accordingly, the invention provides antigenic compositions derived from these microbial pathogens, including whole killed bacterial, viral or fungal species, or components thereof, for the treatment of inflammation or cancer, and methods for using the same. The compositions may for example be derived from endogenous pathogens or exogenous pathogens, as described in more detail below.

Based on observations from treating patients, it was found that administering compositions of killed bacteria which included many of the bacterial species that commonly cause lung infection was surprisingly and unexpectedly effective in improving the clinical course of cancer of the lung. Similarly, it was found that administering compositions including killed Staphylococcus aureus, one of the most common causes of bone, breast, skin, perineal and lymph node infection and septicemia was surprising and unexpectedly effective in improving the clinical course of cancer of the bone, breast, skin, perineum, and lymphoma (cancer of the lymph glands) and multiple myeloma (a type of hematological cancer). Similarly, it was surprisingly and unexpectedly found that administering a composition including Escherichia coli, which is a common cause of colon, kidney, peritoneal, liver, abdominal, pancreatic and ovarian infection, was effective in improving the clinical course of cancer in the colon, kidney, peritoneum, liver, abdominal lymph nodes, pancreas and ovary.

These results indicate that a composition including antigens of pathogenic microbial species that cause infection in a particular tissue or organ will be an effective formulation for treating a cancer in that tissue or organ. For example, cancer in the lung is effectively treated with a microbial composition including one or more pathogenic species that commonly cause lung infection, while cancer in the colon is effectively treated with a composition including pathogenic microbial species that commonly cause colon infections.

Antigenic compositions of the invention may be produced that include antigenic determinants that together are specific for or characteristic of a microbial pathogen. In this context, by “specific”, it is meant that the antigenic determinants are sufficiently characteristic of the pathogen that they could be used to raise an immune response, such as an adaptive immune response, against the pathogen in the patient, if the antigenic determinants were to be administered in an appropriate manner to have that effect. It will be recognized that the antigenic determinants need not be so specific that they are characteristic of only one particular strain or species of pathogen, since even a specific immune response against a particular pathogen may be cross reactive with other closely related organisms that are also naturally pathogenic in the tissue or organ in which the cancer is situated and that the antigenic composition is formulated or selected to target.

In some embodiments, the compositions of pathogenic microbes may be used for treating primary cancer sites and/or sites of metastasis. Thus, for example, the microbial compositions may be used for the treatment of a cancer at a particular site, regardless of whether the cancer is a primary cancer or a metastasis. The composition may be directed to the treatment of each cancer site, or may be a combined composition for both the primary cancer and the metastatic site(s). For example, to treat kidney cancer that has metastasized to the lung and bone, three different compositions, including one or more species that are known to be kidney pathogens, one or more species that are known to be lung pathogens and one or more species that are known to be bone pathogens, or a combined composition thereof may be used. In some embodiments, the compositions may be administered in different locations at the same time or at different times.

For example, for lung cancer with metastasis to the bone, in alternative embodiments, both a microbial composition including one or more bacterial species (or viruses) which commonly cause lung infection and a microbial composition including one or more bacterial species (or viruses) which commonly cause bone infection may be used. Similarly, for colon cancer with metastasis to the lungs, both a pathogenic bacterial (or viral) composition including one or more bacterial species (or viruses) which commonly cause colon infection and a microbial composition including one or more bacterial species (or viruses) which commonly cause lung infection may be used; for prostate cancer with metastasis to the bones, both a pathogenic bacterial (or viral) composition including one or more bacterial species (or viruses) which commonly cause prostate infection and a pathogenic bacterial (or viral) composition including one or more bacterial species (or viruses that commonly cause bone infection may be used. The pathogen for treating immune diseases may be an endogenous organism, which is a natural cause of infection in the organ or tissue in question. The pathogen may be an exogenous organism, which is a natural cause of infection in the tissue or organ in question, and may include, for example, a bacteria, virus, helminth, or fungus.

The following list provides some non-limiting examples of primary cancers and their common sites for secondary spread (metastases):

Primary cancer Common sites for metastases prostate bone, lungs breast bone, lungs, skin, liver, brain lung bone, brain, liver, lungs colon liver, lungs, bone, brain kidney lungs, bone, brain pancreas liver, lungs melanoma lungs, skin, liver, brain uterus lungs, bones, ovaries ovary liver, lung bladder bone, lung, liver head and neck bone, lungs sarcoma lungs, brain stomach liver cervix bone, lungs testes lungs thyroid bone, lungs

In some embodiments, the antigenic compositions may be used for treating or preventing cancers at primary sites or for treating or preventing metastasis. For example, in long-term smokers, an antigenic composition specific for cancer of the lung (for example including antigenic determinants of one or more bacterial species or viruses which commonly cause lung infection) may be used to appropriately stimulate the immune system to defend against the development of cancer within the lung tissue. As another example, an antigenic composition specific for cancer of the breast (for example including antigenic determinants of one or more bacterial species which commonly cause breast infection) could be used to prevent breast cancer in women with a strong family history of breast cancer or a genetic predisposition. In alternative embodiments, an antigenic composition including one or more bacterial species which commonly cause bone infection may be used to prevent or treat bone metastases in a patient with prostate cancer. In further alternative embodiments, an antigenic composition including one or more bacterial species or viruses which commonly cause lung infection may be used to prevent or treat lung metastases in a patient with malignant melanoma.

Various alternative embodiments and examples of the invention are described herein. These embodiments and examples are illustrative and should not be construed as limiting the scope of the invention.

Cancers

Most cancers fall within three broad histological classifications: carcinomas, which are the predominant cancers and are cancers of epithelial cells or cells covering the external or internal surfaces of organs, glands, or other body structures (for e.g., skin, uterus, lung, breast, prostate, stomach, bowel), and which tend to metastasize; carcinomas, which are derived from connective or supportive tissue (for e.g., bone, cartilage, tendons, ligaments, fat, muscle); and hematologic tumors, which are derived from bone marrow and lymphatic tissue. Carcinomas may be adenocarcinomas (which generally develop in organs or glands capable of secretion, such as breast, lung, colon, prostate or bladder) or may be squamous cell carcinomas (which originate in the squamous epithelium and generally develop in most areas of the body). Sarcomas may be osteosarcomas or osteogenic sarcomas (bone), chondrosarcomas (cartilage), leiomyosarcomas (smooth muscle), rhabdomyosarcomas (skeletal muscle), mesothelial sarcomas or mesotheliomas (membranous lining of body cavities), fibrosarcomas (fibrous tissue), angiosarcomas or hemangioendotheliomas (blood vessels), liposarcomas (adipose tissue), gliomas or astrocytomas (neurogenic connective tissue found in the brain), myxosarcomas (primitive embryonic connective tissue), or mesenchymous or mixed mesodermal tumors (mixed connective tissue types). Hematologic tumors may be myelomas, which originate in the plasma cells of bone marrow; leukemias which may be “liquid cancers” and are cancers of the bone marrow and may be myelogenous or granulocytic leukemia (myeloid and granulocytic white blood cells), lymphatic, lymphocytic, or lymphoblastic leukemias (lymphoid and lymphocytic blood cells) or polycythemia vera or erythremia (various blood cell products, but with red cells predominating); or lymphomas, which may be solid tumors and which develop in the glands or nodes of the lymphatic system, and which may be Hodgkin or Non-Hodgkin lymphomas. In addition, mixed type cancers, such as adenosquamous carcinomas, mixed mesodermal tumors, carcinosarcomas, or teratocarcinomas also exist.

Cancers named based on primary site may be correlated with histological classifications. For example, lung cancers are generally small cell lung cancers or non-small cell lung cancers, which may be squamous cell carcinoma, adenocarcinoma, or large cell carcinoma; skin cancers are generally basal cell cancers, squamous cell cancers, or melanomas. Lymphomas may arise in the lymph nodes associated with the head, neck and chest, as well as in the abdominal lymph nodes or in the axillary or inguinal lymph nodes. Identification and classification of types and stages of cancers may be performed by using for example information provided by the Surveillance, Epidemiology, and End Results (SEER) Program of the National Cancer Institute, which is an authoritative source of information on cancer incidence and survival in the United States and is recognized around the world. The SEER Program currently collects and publishes cancer incidence and survival data from 14 population-based cancer registries and three supplemental registries covering approximately 26 percent of the US population. The program routinely collects data on patient demographics, primary tumor site, morphology, stage at diagnosis, first course of treatment, and follow-up for vital status, and is the only comprehensive source of population-based information in the United States that includes stage of cancer at the time of diagnosis and survival rates within each stage. Information on more than 3 million in situ and invasive cancer cases is included in the SEER database, and approximately 170,000 new cases are added each year within the SEER coverage areas. The incidence and survival data of the SEER Program may be used to access standard survival for a particular cancer site and stage. For example, to ensure an optimal comparison group, specific criteria may be selected from the database, including date of diagnosis and exact stage (for example, in the case of the lung cancer example herein, the years were selected to match the time-frame of the retrospective review, and stage 3B and 4 lung cancer were selected; and in the case of the colon cancer example herein, the years were also selected to match the time-frame of the retrospective review, and the stage 4 colon cancer was selected).

Cancers may also be named based on the organ in which they originate i.e., the “primary site,” for example, cancer of the breast, brain, lung, liver, skin, prostate, testicle, bladder, colon and rectum, cervix, uterus, etc. This naming persists even if the cancer metastasizes to another part of the body that is different from the primary site. With the present invention, treatment is directed to the site of the cancer, not type of cancer, so that a cancer of any type that is situated in the lung, for example, would be treated on the basis of this localization in the lung.

A “cancer” or “neoplasm” is any unwanted growth of cells serving no physiological function. In general, a cancer cell has been released from its normal cell division control, i.e., a cell whose growth is not regulated by the ordinary biochemical and physical influences in the cellular environment. Thus, “cancer” is a general term for diseases characterized by abnormal uncontrolled cell growth. In most cases, a cancer cell proliferates to form clonal cells that are malignant. The lump or cell mass, “neoplasm” or “tumor,” is generally capable of invading and destroying surrounding normal tissues. By “malignancy”, as used herein, is meant as an abnormal growth of any cell type or tissue that has a deleterious effect in the organism having the abnormal growth. The term “malignancy” or “cancer” includes cell growths that are technically benign but which carry the risk of becoming malignant. Cancer cells may spread from their original site to other parts of the body through the lymphatic system or blood stream in a process known as “metastasis.” Many cancers are refractory to treatment and prove fatal. Examples of cancers or neoplasms include, without limitation, transformed and immortalized cells, tumors, carcinomas, in various organs and tissues as described herein or known to those of skill in the art.

A “cell” is the basic structural and functional unit of a living organism. In higher organisms, e.g., animals, cells having similar structure and function generally aggregate into “tissues” that perform particular functions. Thus, a tissue includes a collection of similar cells and surrounding intercellular substances, e.g., epithelial tissue, connective tissue, muscle, nerve. An “organ” is a fully differentiated structural and functional unit in a higher organism that may be composed of different types of tissues and is specialized for some particular function, e.g., kidney, heart, brain, liver, etc. Accordingly, by “specific organ, tissue, or cell” is meant herein to include any particular organ, and to include the cells and tissues found in that organ.

“Pathogenic” agents are agents, such as microbes, such as bacteria or viruses, which are known to cause infection in a host in nature, and in this sense, “pathogenic” is used in the context of the present invention to mean “naturally pathogenic”. Although a wide variety of microbes may be capable of causing infection under artificial conditions, such as artificial inoculations of a microbe into a tissue, the range of microbes that naturally cause infection is necessarily limited, and well established by medical practice.

An “infection” is the state or condition in which the body or a part of it is invaded by a pathogenic agent (e.g., a microbe, such as a bacterium) which, under favorable conditions, multiplies and produces effects that are injurious (Taber's Cyclopedic Medical Dictionary, 14th Ed., C. L. Thomas, Ed., F. A. Davis Company, PA, USA). An infection may not always be apparent clinically and may result in only localized cellular injury. Infections may remain subclinical, and temporary if the body's defensive mechanisms are effective. Infections may spread locally to become clinically apparent as an acute, a subacute, or a chronic clinical infection or disease state. A local infection may also become systemic when the pathogenic agent gains access to the lymphatic or vascular system (On-Line Medical Dictionary, http://cancerweb.ncl.ac.uk/omd/). Infection is usually accompanied by inflammation, but inflammation may occur without infection.

“Inflammation” is the characteristic tissue reaction to injury (marked by swelling, redness, heat, and pain), and includes the successive changes that occur in living tissue when it is injured. Infection and inflammation are different conditions, although one may arise from the other (Taber's Cyclopedic Medical Dictionary, supra). Accordingly, inflammation may occur without infection and infection may occur without inflammation (although inflammation typically results from infection by pathogenic bacteria or viruses). Inflammation is characterized by the following symptoms: redness (rubor), heat (calor), swelling (tumor), pain (dolor). Localized visible inflammation on the skin may be apparent from a combination of these symptoms, particularly redness at a site of administration.

Various subjects may be treated in accordance with alternative aspects of the invention. As used herein, a “subject” is an animal, for e.g, a mammal, to whom the specific pathogenic bacteria, bacterial antigens, viruses, viral antigens or compositions thereof of the invention may be administered. Accordingly, a subject may be a patient, e.g., a human, suffering from a cancer, or suspected of having a cancer, or at risk for developing a cancer. A subject may also be an experimental animal, e.g., an animal model of a cancer, as is described in Example 5. In some embodiments, the terms “subject” and “patient” may be used interchangeably, and may include a human, a non-human mammal, a non-human primate, a rat, mouse, dog, etc. A healthy subject may be a human who is not suffering from a cancer or suspected of having a cancer, or who is not suffering from a chronic disorder or condition. A “healthy subject” may also be a subject who is not immunocompromised. By immunocompromised is meant any condition in which the immune system functions in an abnormal or incomplete manner. Immunocompromisation may be due to disease, certain medications, or conditions present at birth. Immunocompromised subjects may be found more frequently among infants, the elderly, and individuals undergoing extensive drug or radiation therapy.

An “immune response” includes, but is not limited to, one or more of the following responses in a mammal: induction or activation of antibodies, neutrophils, monocytes, macrophages (including both M1-like macrophages and M2-like macrophages as described herein), B cells, T cells (including helper T cells, natural killer cells, cytotoxic T cells, γδ T cells), such as induction or activation by the antigen(s) in a composition or vaccine, following administration of the composition or vaccine. An immune response to a composition or vaccine thus generally includes the development in the host animal of a cellular and/or antibody-mediated response to the composition or vaccine of interest. In some embodiments, the immune response is such that it will also result in slowing or stopping the progression of a cancer in the animal. An immune response includes both cellular immune responses and humoral immune responses as understood by those persons skilled in the art.

Bacteria and Bacterial Colonizations and Infections

Most animals are colonized to some degree by other organisms, such as bacteria, which generally exist in symbiotic or commensal relationships with the host animal. Thus, many species of normally harmless bacteria are found in healthy animals, and are usually localized to the surface of specific organs and tissues. Often, these bacteria aid in the normal functioning of the body. For example, in humans, symbiotic Escherichia coli bacteria may be found in the intestine, where they promote immunity and reduce the risk of infection with more virulent pathogens.

Bacteria that are generally harmless, such as Escherichia coli, can cause infection in healthy subjects, with results ranging from mild to severe infection to death. Whether or not a bacterium is pathogenic (i.e., causes infection) depends to some extent on factors such as the route of entry and access to specific host cells, tissues, or organs; the intrinsic virulence of the bacterium; the amount of the bacteria present at the site of potential infection; or the health of the host animal. Thus, bacteria that are normally harmless can become pathogenic given favorable conditions for infection, and even the most virulent bacterium requires specific circumstances to cause infection. Accordingly, microbial species that are members of the normal flora can be pathogens when they move beyond their normal ecological role in the endogenous flora. For example, endogenous species can cause infection outside of their ecological niche in regions of anatomical proximity, for example by contiguous spread. When this occurs, these normally harmless endogenous bacteria are considered pathogenic.

Specific bacterial species and viruses are known to cause infections in specific cells, tissues, or organs in otherwise healthy subjects. Examples of bacteria and viruses that commonly cause infections in specific organs and tissues of the body are listed below; it will be understood that these examples are not intended to be limiting and that a skilled person would be able to readily recognize and identify infectious or pathogenic bacteria that cause infections, or commonly cause infections, in various organs and tissues in healthy adults (and recognize the relative frequency of infection with each bacterial species) based on the knowledge in the field as represented, for example, by the following publications: Manual of Clinical Microbiology 8th Edition, Patrick Murray, Ed., 2003, ASM Press American Society for Microbiology, Washington D.C., USA; Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases 5th Edition, G. L. Mandell, J. E. Bennett, R. Dolin, Eds., 2000, Churchill Livingstone, Philadelphia, Pa., USA, all of which are incorporated by reference herein.

Infections of the skin are commonly caused by the following bacterial species: Staphylococcus aureus, Beta hemolytic streptococci group A, B, C or G, Corynebacterium diptheriae, Corynebacterium ulcerans, or Pseudomonas aeruginosa; or viral pathogens: rubeola, rubella, varicella-zoster, echoviruses, coxsackieviruses, adenovirus, vaccinia, herpes simplex, or parvo B19.

Infections of the soft tissue (e.g., fat and muscle) are commonly caused by the following bacterial species: Streptococcus pyogenes, Staphylococcus aureus, Clostridium perfringens, or other Clostridium spp.; or viral pathogens: influenza, or coxsackieviruses.

Infections of the breast are commonly caused by the following bacterial species: Staphylococcus aureus, or Streptococcus pyogenes.

Infections of the lymph nodes of the head and neck are commonly caused by the following bacterial species: Staphylococcus aureus, or Streptococcus pyogenes; or viral pathogens: Epstein-Barr, cytomegalovirus, adenovirus, measles, rubella, herpes simplex, coxsackieviruses, or varicella-zoster.

Infections of the lymph nodes of the arm/axillae are commonly caused by the following bacterial species: Staphylococcus aureus, or Streptococcus pyogenes; or viral pathogens: measles, rubella, Epstein-Barr, cytomegalovirus, adenovirus, or varicella-zoster.

Infections of the lymph nodes of the mediastinum are commonly caused by the following bacterial species: viridans streptococci, Peptococcus spp., Peptostreptococcus spp., Bacteroides spp., Fusobacterium spp., or Mycobacterium tuberculosis; or viral pathogens: measles, rubella, Epstein-Barr, cytomegalovirus, varicella-zoster, or adenovirus.

Infections of the pulmonary hilar lymph nodes are commonly caused by the following bacterial species: Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae, Klebsiella pneumoniae, Haemophilus influenza, Chlamydophila pneumoniae, Bordetella pertussis or Mycobacterium tuberculosis; or viral pathogens: influenza, adenovirus, rhinovirus, coronavirus, parainfluenza, respiratory syncytial virus, human metapneumovirus, or coxsackievirus.

Infections of the intra-abdominal lymph nodes are commonly caused by the following bacterial species: Yersinia enterocolitica, Yersinia pseudotuberculosis, Salmonella spp., Streptococcus pyogenes, Escherichia coli, Staphylococcus aureus, or Mycobacterium tuberculosis; or viral pathogens: measles, rubella, Epstein-Barr, cytomegalovirus, varicella-zoster, adenovirus, influenza, or coxsackieviruses.

Infections of the lymph nodes of the leg/inguinal region are commonly caused by the following bacterial species: Staphylococcus aureus, or Streptococcus pyogenes; or viral pathogens: measles, rubella, Epstein-Barr, cytomegalovirus, or herpes simplex.

Infections of the blood (i.e., septicemia) are commonly caused by the following bacterial species: Staphylococcus aureus, Streptococcus pyogenes, coagulase-negative staphylococci, Enterococcus spp., Escherichia coli, Klebsiella spp., Enterobacter spp., Proteus spp., Pseudomonas aeruginosa, Bacteroides fragilis, Streptococcus pneumoniae, or group B streptococci; or viral pathogens: rubeola, rubella, varicella-zoster, echoviruses, coxsackieviruses, adenovirus, Epstein-Barr, herpes simplex, or cytomegalovirus.

Infections of the bone are commonly caused by the following bacterial species: Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus agalactiae, other streptococci spp., Escherichia coli, Pseudomonas spp., Enterobacter spp., Proteus spp., or Serratia spp.; or viral pathogens: parvovirus B19, rubella, or hepatitis B.

Infections of the joint are commonly caused by the following bacterial species: Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus agalactiae, other streptococci spp., Escherichia coli, Pseudomonas spp., Enterobacter spp., Proteus spp., Serratia spp., Neisseria gonorrhea, salmonella species, Mycobacterim tuberculosis, Hemophilus influenza; or viral pathogens: parvovirus B19, rubella, hepatitis B; or fungal pathogen: Scedosporium prolificans

Infections of the meninges are commonly caused by the following bacterial species: Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus agalactiae, or Listeria monocytogenes; or viral pathogens: echoviruses, coxsackieviruses, other enteroviruses, or mumps.

Infections of the brain are commonly caused by the following bacterial species: Streptococcus spp. (including S. anginosus, S. constellatus, S. intermedius), Staphylococcus aureus, Bacteroides spp., Prevotella spp., Proteus spp., Escherichia coli, Klebsiella spp., Pseudomonas spp., Enterobacter spp., or Borrelia burgdorferi; or viral pathogens: coxsackieviruses, echoviruses, poliovirus, other enteroviruses, mumps, herpes simplex, varicella-zoster, flaviviruses, or bunyaviruses.

Infections of the spinal cord are commonly caused by the following bacterial species: Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus agalactiae, Listeria monocytogenes, or Borrelia burgdorferi; or viral pathogens: coxsackieviruses, echoviruses, poliovirus, other enteroviruses, mumps, herpes simplex, varicella-zoster, flaviviruses, or bunyaviruses.

Infections of the eye/orbit are commonly caused by the following bacterial species: Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus milleri, Escherichia coli, Bacillus cereus, Chlamydia trachomatis, Haemophilus influenza, Pseudomonas spp., Klebsiella spp., or Treponema pallidum; or viral pathogens: adenoviruses, herpes simplex, varicella-zoster, or cytomegalovirus.

Infections of the salivary glands are commonly caused by the following bacterial species: Staphylococcus aureus, viridans streptococci (e.g., Streptococcus salivarius, Streptococcus sanguis, Streptococcus mutans), Peptostreptococcus spp., or Bacteroides spp., or other oral anaerobes; or viral pathogens: mumps, influenza, enteroviruses, or rabies.

Infections of the mouth are commonly caused by the following bacterial species: Prevotella melaminogenicus, anaerobic streptococci, viridans streptococci, Actinomyces spp., Peptostreptococcus spp., or Bacteroides spp., or other oral anaerobes; or viral pathogens: herpes simplex, coxsackieviruses, or Epstein-Barr.

Infections of the tonsils are commonly caused by the following bacterial species: Streptococcus pyogenes, or Group C or G B-hemolytic streptococci; or viral pathogens: rhinoviruses, influenza, coronavirus, adenovirus, parainfluenza, respiratory syncytial virus, or herpes simplex.

Infections of the sinuses are commonly caused by the following bacterial species: Streptococcus pneumoniae, Haemophilus influenza, Moraxella catarrhalis, α-streptococci, anaerobic bacteria (e.g., Prevotella spp.), or Staphylococcus aureus; or viral pathogens: rhinoviruses, influenza, adenovirus, or parainfluenza.

Infections of the nasopharynx are commonly caused by the following bacterial species: Streptococcus pyogenes, or Group C or G B-hemolytic streptococci; or viral pathogens: rhinoviruses, influenza, coronavirus, adenovirus, parainfluenza, respiratory syncytial virus, or herpes simplex.

Infections of the thyroid are commonly caused by the following bacterial species: Staphylococcus aureus, Streptococcus pyogenes, or Streptococcus pneumoniae; or viral pathogens: mumps, or influenza.

Infections of the larynx are commonly caused by the following bacterial species: Mycoplasma pneumoniae, Chlamydophila pneumoniae, or Streptococcus pyogenes; or viral pathogens: rhinovirus, influenza, parainfluenza, adenovirus, corona virus, or human metapneumovirus.

Infections of the trachea are commonly caused by the following bacterial species: Mycoplasma pneumoniae; or viral pathogens: parainfluenza, influenza, respiratory syncytial virus, or adenovirus.

Infections of the bronchi are commonly caused by the following bacterial species: Mycoplasma pneumoniae, Chlamydophila pneumoniae, Bordetella pertussis, Streptococcus pneumoniae, or Haemophilus influenzae; or viral pathogens: influenza, adenovirus, rhinovirus, coronavirus, parainfluenza, respiratory syncytial virus, human metapneumovirus, or coxsackievirus.

Infections of the lung are commonly caused by the following bacterial species: Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae, Klebsiella pneumoniae, or Haemophilus influenza; or viral pathogens: influenza, adenovirus, respiratory syncytial virus, or parainfluenza.

Infections of the pleura are commonly caused by the following bacterial species: Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, Bacteroides fragilis, Prevotella spp., Fusobacterium nucleatum, peptostreptococcus spp., or Mycobacterium tuberculosis; or viral pathogens: influenza, adenovirus, respiratory syncytial virus, or parainfluenza.

Infections of the mediastinum are commonly caused by the following bacterial species: viridans streptococci, Peptococcus spp., Peptostreptococcus spp., Bacteroides spp., Fusobacterium spp., or Mycobacterium tuberculosis; or viral pathogens: measles, rubella, Epstein-Barr, or cytomegalovirus.

Infections of the heart are commonly caused by the following bacterial species: Streptococcus spp. (including S. mitior, S. bovis, S. sanguis, S. mutans, S. anginosus), Enterococcus spp., Staphylococcus spp., Corynebacterium diptheriae, Clostridium perfringens, Neisseria meningitidis, or Salmonella spp.; or viral pathogens: enteroviruses, coxsackieviruses, echoviruses, poliovirus, adenovirus, mumps, rubeola, or influenza.

Infections of the esophagus are commonly caused by the following bacterial species: Actinomyces spp., Mycobacterium avium, Mycobacterium tuberculosis, or Streptococcus spp.; or viral pathogens: cytomegalovirus, herpes simplex, or varicella-zoster.

Infections of the stomach are commonly caused by the following bacterial species: Streptococcus pyogenes or Helicobacter pylori; or viral pathogens: cytomegalovirus, herpes simplex, Epstein-Barr, rotaviruses, noroviruses, or adenoviruses.

Infections of the small bowel are commonly caused by the following bacterial species: Escherichia coli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, or Shigella flexneri; or viral pathogens: adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, or cytomegalovirus.

Infections of the colon/rectum are commonly caused by the following bacterial species: Escherichia coli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, or Shigella flexneri; or viral pathogens: adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, or cytomegalovirus.

Infections of the anus are commonly caused by the following bacterial species: Streptococcus pyogenes, Bacteroides spp., Fusobacterium spp., anaerobic streptococci, Clostridium spp., Escherichia coli, Enterobacter spp., Pseudomonas aeruginosa, or Treponema pallidum; or viral pathogens: herpes simplex.

Infections of the perineum are commonly caused by the following bacterial species: Escherichia coli, Klebsiella spp., Enterococcus spp., Bacteroides spp., Fusobacterium spp., Clostridium spp., Pseudomonas aeruginosa, anaerobic streptococci, Clostridium spp., or Enterobacter spp.; or viral pathogens: herpes simplex.

Infections of the liver are commonly caused by the following bacterial species: Escherichia coli, Klebsiella spp., Streptococcus (anginosus group), Enterococcus, spp. other viridans streptococci, or Bacteroides spp.; or viral pathogens: hepatitis A, Epstein-Barr, herpes simplex, mumps, rubella, rubeola, varicella-zoster, coxsackieviruses, or adenovirus.

Infections of the gallbladder are commonly caused by the following bacterial species: Escherichia coli, Klebsiella spp., Enterobacter spp., enterococci, Bacteroides spp., Fusobacterium spp., Clostridium spp., Salmonella enteriditis, Yersinia enterocolitica, or Shigella flexneri.

Infections of the biliary tract are commonly caused by the following bacterial species: Escherichia coli, Klebsiella spp., Enterobacter spp., enterococci, Bacteroides spp., Fusobacterium spp., Clostridium spp., Salmonella enteriditis, Yersinia enterocolitica, or Shigella flexneri; or viral pathogens: hepatitis A, Epstein-Barr, herpes simplex, mumps, rubella, rubeola, varicella-zoster, cocsackieviruses, or adenovirus.

Infections of the pancreas are commonly caused by the following bacterial species: Escherichia coli, Klebsiella spp., Enterococcus spp., Pseudomonas spp., Staphylococcal spp., Mycoplasma spp., Salmonella typhi, Leptospirosis spp., or Legionella spp.; or viral pathogens: mumps, coxsackievirus, hepatitis B, cytomegalovirus, herpes simplex 2, or varicella-zoster.

Infections of the spleen are commonly caused by the following bacterial species: Streptococcus spp., Staphylococcus spp., Salmonella spp., Pseudomonas spp., Escherichia coli, or Enterococcus spp.; or viral pathogens: Epstein-Barr, cytomegalovirus, adenovirus, measles, rubella, coxsackieviruses, or varicella-zoster.

Infections of the adrenal gland are commonly caused by the following bacterial species: Streptococcus spp., Staphylococcus spp., Salmonella spp., Pseudomonas spp., Escherichia coli, or Enterococcus spp.; or viral pathogens: varicella-zoster.

Infections of the kidney are commonly caused by the following bacterial species: Escherichia coli, Proteus mirabilis, Proteus vulgatus, Providentia spp., Morganella spp., Enterococcus faecalis, or Pseudomonas aeruginosa; or viral pathogens: BK virus, or mumps.

Infections of the ureter are commonly caused by the following bacterial species: Escherichia coli, Proteus mirabilis, Proteus vulgatus, Providentia spp., Morganella spp., or Enterococcus spp.

Infections of the bladder are commonly caused by the following bacterial species: Escherichia coli, Proteus mirabilis, Proteus vulgatus, Providentia spp., Morganella spp., Enterococcus faecalis, or Corynebacterium jekeum; or viral pathogens: adenovirus, or cytomegalovirus.

Infections of the peritoneum are commonly caused by the following bacterial species: Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumonia, Escherichia coli, Klebsiella spp., Proteus spp., enterococci, Bacteroides fragilis, Prevotella melaminogenica, Peptococcus spp., Peptostreptococcus spp., Fusobacterium spp., or Clostridium spp.

Infections of the retroperitoneal area are commonly caused by the following bacterial species: Escherichia coli, or Staphylococcus aureus.

Infections of the prostate are commonly caused by the following bacterial species: Escherichia coli, Klebsiella spp., Enterobacter spp., Proteus mirabilis, enterococci spp., Pseudomonas spp., Corynebacterium spp., or Neisseria gonorrhoeae; or viral pathogens: herpes simplex.

Infections of the testicle are commonly caused by the following bacterial species: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus spp., Streptococcus spp., or Salmonella enteriditis; or viral pathogens: mumps, coxsackievirus, or lymphocytic choriomeningitis virus.

Infections of the penis are commonly caused by the following bacterial species: Staphylococcus aureus, Streptococcus pyogenes, Neisseria gonorrhoeae, or Treponema pallidum; or viral pathogens: herpes simplex.

Infections of the ovary/adnexae are commonly caused by the following bacterial species: Neisseria gonorrhoeae, Chlamydia trachomatis, Gardenerella vaginalis, Prevotella spp., Bacteroides spp., Peptococcus spp. Streptococcus spp., or Escherichia coli.

Infections of the uterus are commonly caused by the following bacterial species: Neisseria gonorrhoeae, Chlamydia trachomatis, Gardenerella vaginalis, Prevotella spp., Bacteroides spp., Peptococcus spp., Streptococcus spp., or Escherichia coli.

Infections of the cervix are commonly caused by the following bacterial species: Neisseria gonorrhoeae, Chlamydia trachomatis, or Treponema pallidum; or viral pathogens: herpes simplex.

Infections of the vagina are commonly caused by the following bacterial species: Gardenerella vaginalis, Prevotella spp., Bacteroides spp., peptococci spp., Escherichia coli, Neisseria gonorrhoeae, Chlamydia Trachomatis, or Treponema pallidum; or viral pathogens: herpes simplex.

Infections of the vulva are commonly caused by the following bacterial species: Staphylococcus aureus, Streptococcus pyogenes, or Treponema pallidum; or viral pathogens: herpes simplex.

Bacterial Strains/Viral Subtypes

It will be understood by a skilled person in the art that bacterial species are classified operationally as collections of similar strains (which generally refers to groups of presumed common ancestry with identifiable physiological but usually not morphological distinctions, and which may be identified using serological techniques against bacterial surface antigens). Thus, each bacterial species (e.g., Streptococcus pneumoniae) has numerous strains (or serotypes), which may differ in their ability to cause infection or differ in their ability to cause infection in a particular organ/site. For example, although there are at least 90 serotypes of Streptococcus pneumoniae, serotypes 1, 3, 4, 7, 8, and 12 are most frequently responsible for pneumococcal disease in humans.

As a second example, certain strains of Escherichia coli, referred to as extraintestinal pathogenic E. coli (ExPEC), are more likely to cause urinary tract infection or other extraintestinal infections such as neonatal meningitis, whereas other strains, including enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC), Shiga toxin-producing E. coli (STEC), enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC) and diffuse adhering E. coli (DAEC) are more likely to cause gastrointestinal infection/diarrhea. Even among the sub-category of ExPEC strains, specific virulence factors (e.g., production of type-1 fimbriae) enable certain strains to be more capable of causing infection of the bladder, while other virulence factors (e.g., production of P fimbriae) enable other strains to be more capable of causing infection in the kidneys. In accordance with the present invention, an ExPEC strain(s) that is more likely to cause infection in the bladder may be chosen for a formulation to target bladder cancer, whereas an ExPEC strain(s) that is more likely to cause infection in the kidney may be chosen for a formulation to target kidney cancer. Likewise, one or more of an ETEC, EPEC, EHEC, STEC, EAEC, EIEC or DAEC strains of E. coli (i.e., strains that cause colon infection), may be chosen for a formulation to treat colon cancer.

Similarly, there may be numerous subtypes of specific viruses. For example, there are three types of influenza viruses, influenza A, influenza B and influenza C, which differ in epidemiology, host range and clinical characteristics. For example, influenza A is more likely to be associated with viral lung infection, whereas influenza B is more likely to be associated with myositis (i.e., muscle infection). Furthermore, each of these three types of influenza virus have numerous subtypes, which also may differ in epidemiology, host range and clinical characteristics. In accordance with the present invention, one may choose an influenza A subtype most commonly associated with lung infection to target lung cancer, whereas one may choose an influenza B strain most commonly associated with myositis to treat cancer of the muscle/soft tissues.

It is understood that a clinical microbiologist skilled in the art would therefore be able to select, based on the present disclosure and the body of art relating to bacterial strains for each species of bacteria (and viral subtypes for each type of virus), the strains of a particular bacterial species (or subtype of a particular virus) to target a specific organ or tissue.

Bacterial Compositions, Dosages, and Administration

The compositions of the invention include antigens of pathogenic microbial (bacterial or viral) species that are pathogenic in a specific tissue or organ. The compositions may include whole bacterial species, or may include extracts or preparations of the pathogenic bacterial species of the invention, such as cell wall or cell membrane extracts, or whole cells, or exotoxins, or whole cells and exotoxins. The compositions may also include one or more isolated antigens from one or more of the pathogenic bacterial species of the invention; in some embodiments, such compositions may be useful in situations where it may be necessary to precisely administer a specific dose of a particular antigen, or may be useful if administering a whole bacterial species or components thereof (e.g., toxins) may be harmful. Pathogenic bacterial species may be available commercially (from, for example, ATCC (Manassas, Va., USA), or may be clinical isolates from subjects having a bacterial infection of a tissue or organ (e.g., pneumonia).

The microbial compositions of the invention can be provided alone or in combination with other compounds (for example, nucleic acid molecules, small molecules, peptides, or peptide analogues), in the presence of a liposome, an adjuvant, or any pharmaceutically acceptable carrier, in a form suitable for administration to mammals, for example, humans. As used herein “pharmaceutically acceptable carrier” or “excipient” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. The carrier can be suitable for any appropriate form of administration, including subcutaneous, intradermal, intravenous, parenteral, intraperitoneal, intramuscular, sublingual, inhalational, intratumoral or oral administration. Pharmaceutically acceptable carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound (i.e., the specific bacteria, bacterial antigens, or compositions thereof of the invention), use thereof in the pharmaceutical compositions of the invention is contemplated. Supplementary active compounds can also be incorporated into the compositions.

If desired, treatment with bacterial antigens according to the invention may be combined with more traditional and existing therapies for cancer, such as chemotherapy, radiation therapy, surgery, etc., or with any other therapy intended to stimulate the immune system, reduce inflammation or otherwise benefit the subject, such as nutrients, vitamins and supplements. For example, vitamin A, vitamin D, vitamin E, vitamin C, vitamin B complex, selenium, zinc, co-enzyme Q10, beta carotene, fish oil, curcumin, green tea, bromelain, resveratrol, ground flaxseed, garlic, lycopene, milk thistle, melatonin, other antioxidants, cimetidine, indomethacin, or COX-2 Inhibitors (e.g., Celebrex™ [celecoxib] or Vioxx™ [rofecoxib]) may be also be administered to the subject.

Conventional pharmaceutical practice may be employed to provide suitable formulations or compositions to administer the compounds to subjects suffering from a cancer. Any appropriate route of administration may be employed, for example, parenteral, intravenous, intradermal, subcutaneous, intramuscular, intracranial, intraorbital, ophthalmic, intraventricular, intracapsular, intraspinal, intrathecal, intracisternal, intraperitoneal, intranasal, inhalational, aerosol, topical, intratumoral, sublingual or oral administration. Therapeutic formulations may be in the form of liquid solutions or suspensions; for oral administration, formulations may be in the form of tablets or capsules; for intranasal formulations, in the form of powders, nasal drops, or aerosols; and for sublingual formulations, in the form of drops, aerosols or tablets.

Methods well known in the art for making formulations are found in, for example, “Remington's Pharmaceutical Sciences” (20th edition), ed. A. Gennaro, 2000, Mack Publishing Company, Easton, Pa. Formulations for parenteral administration may, for example, contain excipients, sterile water, or saline, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, or hydrogenated napthalenes. Biocompatible, biodegradable lactide polymer, lactide/glycolide copolymer, or polyoxyethylene-polyoxypropylene copolymers may be used to control the release of the compounds. Other potentially useful parenteral delivery systems for include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Formulations for inhalation may contain excipients, for example, lactose, or may be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate and deoxycholate, or may be oily solutions for administration in the form of nasal drops, or as a gel. For therapeutic or prophylactic compositions, the pathogenic bacterial species are administered to an individual in an amount effective to stop or slow progression or metastasis of the cancer, or to increase survival of the subject (relative to, for example, prognoses derived from the SEER database) depending on the disorder.

An “effective amount” of a pathogenic microbial species or antigen thereof according to the invention includes a therapeutically effective amount or a prophylactically effective amount. A “therapeutically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result, such as reduction or elimination of the cancer cells or tumors, prevention of carcinogenic processes, slowing the growth of the tumour, or an increase in survival time beyond that which is expected using for example the SEER database. A therapeutically effective amount of a pathogenic microbial (bacterial or viral) species or antigen(s) thereof may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the compound to elicit a desired response in the individual. Dosage regimens may be adjusted to provide the optimum therapeutic response. A therapeutically effective amount may also be one in which any toxic or detrimental effects of the pathogenic bacterial species or virus or antigen thereof are outweighed by the therapeutically beneficial effects. A “prophylactically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result, such as prevention of cancer, prevention of metastasis, slowing the growth of the tumour, reduction or elimination of the cancer cells, tissues, organs, or tumors, or an increase in survival time beyond that which is expected using for example the SEER database. Typically, a prophylactic dose is used in subjects prior to or at an earlier stage of cancer, so that a prophylactically effective amount may be less than a therapeutically effective amount.

For administration by subcutaneous or intradermal injection, an exemplary range for therapeutically or prophylactically effective amounts of one or more pathogenic bacterial species may be about 1 million to 100,000 million organisms per ml, or may be 100 million to 7000 million organisms per ml, or may be 500 million to 6000 million organisms per ml, or may be 1000 million to 5000 million organisms per ml, or may be 2000 million to 4000 million organisms per ml, or any integer within these ranges. The total concentration of bacteria per ml may range from 1 million to 100,000 million organisms per ml, or may be 50 million to 7000 million organisms per ml, or may be 100 million to 6000 million organisms per ml, or may be 500 million to 5000 million organisms per ml, or may be 1000 million to 4000 million organisms per ml, or any integer within these ranges. The range for therapeutically or prophylactically effective amounts of antigens of a pathogenic bacterial species may be any integer from 0.1 nM-0.1 M, 0.1 nM-0.05M, 0.05 nM-15 μM or 0.01 nM-10 μM.

It is to be noted that dosage concentrations and ranges may vary with the severity of the condition to be alleviated, or may vary with the subject's immune response. In general, the goal is to achieve an adequate immune response. For administration by subcutaneous or intradermal infection, the extent of an immune response may be determined, for example, by size of delayed local immune skin reaction at the site of injection (e.g., from 0.25 inch to 4 inch diameter). The dose required to achieve an appropriate immune response may vary depending on the individual (and their immune system) and the response desired. Standardized dosages may also be used. In the context of subcutaneous or intradermal administration, if the goal is to achieve a 2 inch local skin reaction, the total bacterial composition dose may, for example, range from 2 million bacteria (e.g., 0.001 ml of a vaccine with a concentration of 2,000 million organisms per ml) to more than 20,000 million bacteria (e.g., 1 ml of a vaccine with a concentration of 20,000 million organisms per ml). The concentrations of individual bacterial species or antigens thereof within a composition may also be considered. For example, if the concentration of one particular pathogenic bacterial species, cell size of that species or antigenic load thereof is much higher relative to the other pathogenic bacterial species in the vaccine, then the local immune skin reaction of an individual may be likely due to its response to this specific bacterial species. In some embodiments, the immune system of an individual may respond more strongly to one bacterial species within a composition than another, depending for example on past history of exposure to infection by a particular species, so the dosage or composition may be adjusted accordingly for that individual. However, in some embodiments detailed herein, an immune response will not be monitored by way of a skin reaction. For example, in some mouse models utilized herein, the effective treatment of such animals with antigenic compositions may not result in corresponding skin reactions. A person skilled in the art will understand that there are alternate ways in which an immune response can be monitored beside relying on the presence or absence of a skin reaction.

For any particular subject, the timing and dose of treatments may be adjusted over time (e.g., timing may be daily, every other day, weekly, monthly) according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions. For example, in the context of subcutaneous or intradermal administration, the compositions may be administered every second day. An initial dose of approximately 0.05 ml may be administered subcutaneously, followed by increases from 0.01-0.02 ml every second day until an adequate skin reaction is achieved at the injection site (for example, a 1 inch to 2 inch diameter delayed reaction of visible redness at the injection site). Once this adequate immune reaction is achieved, this dosing is continued as a maintenance dose. The maintenance dose may be adjusted from time to time to achieve the desired visible skin reaction (inflammation) at the injection site. Dosing may be for a dosage duration, for example of at least 1 week, 2 weeks, 2 months, 6 months, 1, 2, 3, 4, or 5 years or longer.

Oral dosages may for example range from 10 million to 1,000,000 million organisms per dose, comprising antigenic determinants of one or more species. Oral dosages may be given, for example, from 4 times per day, daily or weekly. Dosing may be for a dosage duration, for example of at least 1 week, 2 weeks, 2 months, 6 months, 1, 2, 3, 4, or 5 years or longer.

In some embodiments, the invention may include antigenic compositions administered sublingually or by inhalation, or administered to one or more epithelial tissues (i.e., skin by intradermal or subcutaneous injection; lung epithelium by inhalation; gastrointestinal mucosa by oral ingestion; mouth mucosa by sublingual administration) simultaneously or sequentially. Accordingly, in some embodiments the antigenic compositions of the invention are administered so as to provoke an immune response in an epithelial tissue. In some embodiments, one or more epithelial routes of administration may be combined with one or more additional routes of administration, such as intratumoral, intramuscular or intravenous administration.

In various aspects of the invention, the antigenic compositions that are administered to a patient may be characterized as having an antigenic signature, i.e., a combination of antigens or epitopes that are sufficiently specific that the antigenic composition is capable of eliciting an immune response that is specific to a particular pathogen, such as an adaptive immune response. A surprising and unexpected aspect of the invention is that the non-adaptive or non-specific activation of the immune response that is mediated by these specific antigenic compositions is effective to treat cancers situated in the tissues in which the particular pathogen is pathogenic.

Routes of administration and dosage ranges set forth herein are exemplary only and do not limit the route of administration and dosage ranges that may be selected by medical practitioners. The amount of active compound (e.g., pathogenic bacterial species or viruses or antigens thereof) in the composition may vary according to factors such as the disease state, age, sex, and weight of the individual. Dosage regimens may be adjusted to provide the optimum therapeutic response. For example, a single bolus may be administered, several divided doses may be administered over time or the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It may be advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage.

In the case of antigenic formulations (analogous to a vaccine), an immunogenically effective amount of a compound of the invention can be provided, alone or in combination with other compounds, with an immunological adjuvant. The compound may also be linked with a carrier molecule, such as bovine serum albumin or keyhole limpet hemocyanin to enhance immunogenicity. An antigenic composition (“vaccine”) is a composition that includes materials that elicit a desired immune response. An antigenic composition may select, activate or expand, without limitation: memory B, T cells, neutrophils, monocytes or macrophages of the immune system to, for example, reduce or eliminate the growth or proliferation of cancerous cells or tissue. In some embodiments, the specific pathogenic microbe, virus, viral antigens, bacteria, bacterial antigens, or compositions thereof of the invention are capable of eliciting the desired immune response in the absence of any other agent, and may therefore be considered to be an antigenic composition. In some embodiments, an antigenic composition includes a suitable carrier, such as an adjuvant, which is an agent that acts in a non-specific manner to increase the immune response to a specific antigen, or to a group of antigens, enabling the reduction of the quantity of antigen in any given vaccine dose, or the reduction of the frequency of dosage required to generate the desired immune response. A bacterial antigenic composition may include live or dead bacteria capable of inducing an immune response against antigenic determinants normally associated with the bacteria. In some embodiments, an antigenic composition may include live bacteria that are of less virulent strains (attenuated), and therefore cause a less severe infection. In some embodiments the antigenic composition may include live, attenuated or dead viruses capable of inducing an immune response against antigenic determinants normally associated with the virus.

An antigenic composition comprising killed bacteria for administration by injection may be made as follows. The bacteria may be grown in suitable media, and washed with physiological salt solution. The bacteria may then be centrifuged, resuspended in saline solution, and killed with heat. The suspensions may be standardized by direct microscopic count, mixed in required amounts, and stored in appropriate containers, which may be tested for safety, shelf life, and sterility in an approved manner. In addition to the pathogenic bacterial species and/or antigens thereof, a killed bacterial vaccine suitable for administration to humans may include 0.4% phenol preservative and/or 0.9% sodium chloride. The bacterial vaccine may also include trace amounts of brain heart infusion (beef), peptones, yeast extract, agar, sheep blood, dextrose, sodium phosphate and/or other media components.

In some embodiments, the bacterial vaccine may be used in tablet or capsule form or drops for oral ingestion, as an aerosol for inhalation, or as drops, aerosol or tablet form for sublingual administration.

In antigenic compositions comprising bacteria, the concentrations of specific bacterial species in compositions for subcutaneous or intradermal injection may be about 1 million to 100,000 million organisms per ml, or may be 100 million to 7000 million organisms per ml, or may be 500 million to 6000 million organisms per ml, or may be 1000 million to 5000 million organisms per ml, or may be 2000 million to 4000 million organisms per ml, or any integer within these ranges. The total concentration of bacteria per ml may range from 1 million to 100,000 million organisms per ml, or may be 50 million to 7000 million organisms per ml, or may be 100 million to 6000 million organisms per ml, or may be 500 million to 5000 million organisms per ml, or may be 1000 million to 4000 million organisms per ml, or any integer within these ranges.

In some embodiments, a selected killed bacterial vaccine for cancer of the lung tissue would include the common bacterial lung pathogens, and may for example be:

bacteria per ml Streptococcus pneumoniae 600 million Haemophilus influenzae 400 million Moraxella catarrhalis 400 million Mycoplasma pneumoniae 300 million Klebsiella pneumoniae 300 million total: 2,000 million   or alternatively Streptococcus pneumoniae 600 million Haemophilus influenzae 300 million Moraxella catarrhalis 300 million Mycoplasma pneumoniae 400 million Klebsiella pneumoniae 400 million total: 2,000 million   In some selected embodiments, a selected killed bacterial vaccine for cancer of the lung tissue would include only more common bacterial lung pathogens, and may for example be:

bacteria per ml Streptococcus pneumoniae 800 million Haemophilus influenzae 600 million Moraxella catarrhalis 600 million total: 2,000 million   or alternatively: Streptococcus pneumoniae 800 million Mycoplasma pneumoniae 600 million Klebsiella pneumoniae 600 million total: 2,000 million  

In further selected embodiments, a selected killed bacterial vaccine for cancer of the lung tissue would include only the most common bacterial lung pathogen, and may be:

bacteria per ml Streptococcus pneumoniae 2,000 million total: 2,000 million or Klebsiella pneumoniae or 2,000 million total: 2,000 million or Mycoplasma pneumoniae 2,000 million total: 2,000 million

In some embodiments, an antigenic microbial composition for treating cancer at a particular site (e.g., cancer of the lung tissue) may include pathogenic microbes that commonly, more commonly, or most commonly cause infection in that tissue or organ (e.g., infection in the lung tissue i.e., pneumonia).

In general, the pathogenic bacterial species and antigens thereof of the invention should be used without causing substantial toxicity. Toxicity of the compounds of the invention can be determined using standard techniques, for example, by testing in cell cultures or experimental animals and determining the therapeutic index, i.e., the ratio between the LD50 (the dose lethal to 50% of the population) and the LD100 (the dose lethal to 100% of the population).

In some aspects, the invention involves the use of an anti-inflammatory in conjunction with vaccinations. In these embodiments, a wide variety of anti-inflammatory treatments may be employed, including effective amounts of non-steroidal anti-inflammatory drugs (NSAIDs), including but not limited to: diclofenac potassium, diclofenac sodium, etodolac, indomethicin, ketorolac tromethamine, sulindac, tometin sodium, celecoxib, meloxicam, valdecoxib, floctafenine, mefenamic acid, nabumetone, meloxicam, piroxicam, tenoxicam, fenoprofen calcium, flubiprofen, ibuprofen, ketoprofen, naproxen, naproxen sodium, oxaprozin, tiaprofenic acid, acetylsalicylic acid, diflunisal, choline magnesium trisalicylate, choline salicylate, triethanolamine salicylate, COX1 inhibitors, COX2 inhibitors (e.g., Vioxx™, and Celebrex™). A variety of herbs and natural health products may also be used to provide anti-inflammatory treatment, including but not limited to: green tea, fish oil, vitamin D, antioxidant vitamins and minerals (e.g., B carotene, vitamin A, vitamin C, vitamin D, vitamin E, co-enzyme Q10, selenium, etc.), resveratrol, turmeric, bromelain, boswellia, feverfew, quercetin, ginger, rosemary, oregano, cayenne, clove, nutmeg, willowbark. Alternative anti-inflammatory modalities may also include lifestyle modifications, such as: exercise, weight loss, smoking cessation, stress reduction, seeking social support, treatment of depression, stress management, abdominal breath work and dietary change (such as adopting a mediterranean diet, a low glycemic diet, eating non-charred foods, including foods having omega-3 fatty acids).

As detailed herein and in an aspect of the invention, a method of comparing immune responses is provided. The method involves administering to an animal having an organ or tissue a medicament having an antigenic composition, as defined herein. The antigenic composition may have antigenic determinants selected or formulated so that together the antigenic determinants are specific for at least one microbial pathogen that is pathogenic in the organ or tissue, extracting a quantifiable immune sample from the organ or tissue, measuring a characteristic of the immune response in the organ or tissue in the quantifiable immune sample following the administration of the medicament, and, comparing the characteristic of the immune response in the quantifiable immune sample to a corresponding characteristic of the immune response in a reference immune sample obtained from a corresponding organ or tissue. As used herein, an immune sample would contain sufficient biological material to determine a characteristic of an immune response. As used herein, a “characteristic” of an immune response can include, without limitation, the particular number of a particular immune cell type (e.g., macrophage), or a particular cellular marker (e.g., upregulation of an integrin) or gene product (e.g., a cytokine). The foregoing is provided as an example and is non-limiting.

Optionally, the reference immune sample may be obtained from the corresponding organ or tissue in the animal prior to the step of administering the medicament. In another aspect, the reference immune sample may be obtained from the corresponding organ or tissue in a second animal such that it is specifically contemplated that at least two animals (i.e., an animal from which a reference immune sample is obtained and a second animal from which a quantifiable immune sample) could be used in the methods described herein. Optionally, the animal may have a cancer situated in the organ or tissue.

Comparing the characteristic of the immune response may involve comparing, in the quantifiable and reference immune samples, an indication of the numbers of any one or more of the following cells as these cells are known to those skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages.

Those persons skilled in the art will appreciate that macrophages can be defined as either “M1-like macrophages” or “M2-like macrophages”. For example, M1-like macrophages are generally understood by those persons skilled in the art to promote a Th1 CD4+ T cell-mediated response (see, for e.g., Biswas and Mantovani (2010), Nature Immunology 10:889-96). Moreover, M1-like macrophages are generally understood to have efficient antigen presentation capacity, and to be proficient at killing intracellular pathogens (for e.g., viruses). Moreover, M1-like macrophages are generally understood to be proficient, at least as compared with M2-like macrophages, in playing an immunological role in tumour destruction. Those skilled in the art will appreciate that there are numerous biological markers which can be employed to differentiate between M1-like macrophages and M2-like macrophages. For example, and as detailed herein, the expression of Nos2 is generally understood to correlate with an M1-like macrophage as compared with an M2-like macrophage (see, for e.g., Laskin et al. (2010) Annual Rev. Pharmacol. Toxicol. 51: 267-288). Further, and for example, M1-like macrophages are generally understood to produce IL-12 and to be effectively activated by IFN-γ through the IFN-γR (Biswas and Mantovain, supra).

In contrast to M1-like macrophages, those persons skilled in the art will generally understand that M2-like macrophages promote a Th2 CD4+ T cell-mediated response (see, generally: Biswas and Mantovani (2010), Nature Immunology 10:889-96). Moreover, M2-like macrophages are generally understood to be effective and encapsulating and clearing extracellular parasites etc. Further, and in comparison to M1-like macrophages, M2-like macrophages are generally understood by those persons skilled in the art as playing a more significant role in immunoregulation both with respect to T_(reg) and B cells (Biswas and Mantovain, supra). Those persons skilled in the art will appreciate that there are numerous biological markers which can be employed to differentiate between M2-like macrophages and M1-like macrophages. For example, and as described herein, a diminished expression of Nos2 will generally be understood to correlate with M2-like macrophages as compared with higher expression being generally found in M1-like macrophages. Further, and as detailed in experiments herein, the expression of CD206 is generally understood as correlating with M2-like macrophages (see, for e.g., Choi et al. (2010) Gastroenterology 138(7) 2399-409). Further, and as detailed in experiments herein, the expression of F4/80 is generally understood to correlate with M2-like macrophages. Further, and for example, M2-like macrophages are generally understood to be effectively activated by IL-4 or by IL-13 through IL-4Rα (Biswas and Mantovain, supra).

Further, comparing the characteristic of the immune response may involve comparing a shift in an activation state of macrophages. The shift in the activation state of macrophages may optionally be characterized as a shift from M2-like macrophages to M1-like macrophages or vice versa. Those persons skilled in the art will appreciate that there are numerous biological markers that can be employed to monitor the activation of macrophages. As detailed herein, those skilled in the art will appreciate that defining a macrophage as being activated towards either a M1-like phenotype or a M2-like phenotype can be accomplished by choosing markers that are known to associate with either of the respective phenotypes described herein. Diseases which have been associated with M1 and M2 macrophages include at least the following: atherosclerosis (see, for e.g., Hirata et al. (2011) J. Am. Coll. Cardiol. 58(3): 248-255), allergic asthma (see, for e.g., Moreira and Hogaboam (2011) J. Interferon. Cytokine Res. 31(6): 485-91), autoimmune prostatitis (see, for e.g., Zhang and Schluesener (2011) Prostate), colitis (see, for e.g., Waddell et al. (2011) J. Immunol. 186(10): 5993-6003), COPD (see, for e.g., Kunz et al. (2011) Respir. Res. 22: 34), glomerulonephritis (see, for e.g., Fujita et al. (2010) Am. J. Pathol. 177(3): 1143-54), inflammatory bowel disease (see, for e.g., Wendelsdorf et al. (2010) J. Theor. Biol. 264(4): 1225-39), chronic lung inflammation (see, for e.g., Redente et al. (2010) J. Leukoc. Blol. 88(1): 159-68), steatohepatitis (see, for e.g., Rensen et al. (2009) Am. J. Pathol. 175(4): 1473-82), pancreatitis (see, for e.g., Gea-Sorli and Closa (2009) BMC Immunol. 31: 42), mycocarditis (see, for e.g., Li et al. (2009) Circ. Res. 105(4): 353-64), liver fibrosis (see, for e.g., Heymann et al. (2009) Inflamm. Allergy Drug Targets 8(4): 307-18), cystic fibrosis (see, for e.g., Meyer et al. (2009) Am. J. Respir. Cell Mol. Biol. 41(5): 590-602), inflammatory renal disease (see, for e.g., Wang et al. (2007) Kidney Int 72(3): 290-299), and silicosis (see, for e.g., Misson et al. (2004) J. Leukoc. Biol. 76(5): 926-232).

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cellular markers on any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. A person skilled in the art will appreciate that there are numerous cell markers (both extracellular and intracellular) that can be selected which can identify an immune response. For example, as described herein, the marker CD206 is generally understood as correlating with M2-like macrophages (see, for e.g., Choi et al. (2010) Gastroenterology 138(7) 2399-409).

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cytokines produced by any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Those persons skilled in the art will appreciate that cytokines refer to small cell-signalling protein molecules and that there are numerous cytokines known in the art. For example, cytokines have been grouped into type 1 and type 2 classifications based on their role in immunological responses. Common type 1 cytokines include IFN-γ and TGF-β. Common type 2 cytokines include, but are not limited to IL-4 and IL-13. Cytokines can be detected by numerous methodologies known to those persons skilled in the art. For example, and as detailed herein, ELISA experiments were utilized to determine cytokine production from lung tissue (see, for e.g., FIG. 27).

As detailed herein, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages as has been defined herein. Optionally, the cytokines are produced as a result of a shift in an activation state of the macrophages. Optionally, the macrophages shift from being M2-like macrophages to being M1-like macrophages. Further and optionally, the macrophages shift from being M1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, differential gene expression produced by any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. The term “differential gene expression” is understood to mean an appreciable difference between the expression of a particular gene of interest from at least two experimental conditions. For example, if under a first experimental condition a particular gene has a defined expression level as defined by gene expression methods used by those persons skilled in the art and if under a second experimental condition the same gene has an appreciable difference in its expression level, then there is differential expression of the gene of interest. Those persons skilled in the art will understand that there are numerous methodologies with which to detect differential gene expression. For example, commercially available quantitative PCR techniques can be used as detailed herein with respect to determining the relative Nos2/Arg1 ratios (see, for e.g., FIG. 29). Optionally, the differential gene expression is produced as a result of a shift in an activation state of the macrophages. Optionally, macrophages may shift from being M2-like macrophages to being M1-like macrophages as those terms have been defined herein.

In another embodiment, the medicament may be administered at an administration site in successive doses given at a dosage interval of between one hour and one month, over a dosage duration of at least one week. Optionally, the medicament may be administered intradermally or subcutaneously. Optionally, the medicament may be administered in a dose so that each dose is effective to cause a visible localized inflammatory immune response at the administration site. Optionally, the medicament may be administered so that visible localized inflammation at the administration site occurs within 1 to 48 hours. However, a visible localized inflammatory immune response may not always be present in all circumstances despite an immune response being initiated. Those skilled in the art will appreciate that there are other methods by which the mounting of an immune response can be monitored. For example, the profile (and relative change in characterization) of immune cells from a subject undergoing an immune reaction can be compared with those from a subject that is not undergoing an immune reaction.

Further and optionally with respect to the methods disclosed herein, the animal may be a mammal. Optionally, the animal may be a human or a mouse. The foregoing are provided as examples and are not meant to be limiting.

In another aspect, a method of selecting a therapeutic preparation suitable for treating an individual for a cancer in a specific organ or tissue is provided. The method involves providing an animal having a cancer situated in a specific organ or tissue, providing a test preparation having one or more antigenic determinants of a microbial pathogen which is pathogenic in the corresponding specific organ or tissue in a healthy individual, measuring a characteristic of the immune response in a reference immune sample obtained from the organ or tissue of the animal, administering the test preparation to the animal, measuring a characteristic of the immune response in a quantifiable immune sample obtained from a corresponding organ or tissue of the animal, comparing the characteristic of the immune response in the in the reference and quantifiable immune samples, and treating an enhanced characteristic of the immune response in the quantifiable immune sample compared to the reference immune sample as an indication of the suitability of the test preparation as a therapeutic preparation. Optionally, the animal is sacrificed before the quantifiable immune sample has been obtained.

Optionally, comparing the characteristic of the immune response may involve comparing, in the quantifiable and reference immune samples, an indication of the numbers of any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages as those terms have been defined herein. Optionally, comparing the characteristic of the immune response may involve comparing a shift in an activation state of macrophages. Optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. Further and optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cellular markers on any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages as those terms have been defined herein.

Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cytokines produced by any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages as those terms have been defined herein. Optionally, the cytokines are produced as a result of a shift in an activate state of the macrophages. Optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages.

Further and optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, differential gene expression produced by any one or more of the following cells: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages as those terms have been defined herein. Optionally, the differential gene expression may be produced as a result of a shift in an activation state of the macrophages. Optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. Further and optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

In another aspect, a method of selectively targeting an immune response to a cancerous tissue or an organ in a human subject is provided. The method involves administering to the subject a medicament having an effective amount of a microbial pathogen antigenic composition, wherein the microbial pathogen may be pathogenic in the specific cancerous organ or tissue of the subject and the antigenic composition comprises antigenic determinants that together are specific for the microbial pathogen. Optionally, the antigenic composition may include a whole killed bacterial cell composition. Optionally, the medicament may be administered to the subject in an amount and for a time that is effective to up-regulate an immune response in the cancerous organ or tissue of the subject. Optionally, the method may further involve measuring a characteristic of the immune response.

In another aspect, a method for treating a human subject for a cancer situated in a tissue or an organ is provided. The method involves administering to the subject a medicament having an effective amount of a microbial pathogen antigenic composition comprising a whole killed bacterial cell composition, wherein the microbial pathogen is pathogenic in the specific organ or tissue of the subject within which the cancer is situated. The medicament may be administered to the subject in an amount and for a time that is effective to modulate an immune response. Optionally, the modulation of the immune response may involve a shift in the activation state of macrophages. Optionally, the modulation of the immune response may involve shifting from a M2-like macrophage response to a M1-like macrophage response. The modulation of the immune responses may involve shifting from a M1-like macrophage response to a M2-like macrophage response. Optionally, the method may further involve measuring a characteristic of the immune response.

Optionally, comparing the characteristic of the immune response may involve comparing, in the quantifiable and reference immune samples, an indication of the numbers of any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages as those terms have been defined herein. Optionally, comparing the characteristic of the immune response may involve comparing a shift in an activation state of macrophages. Further and optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. Optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

Further and optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cellular markers on any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages as those terms have been defined herein. Optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, cytokines produced by any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Further, cytokines may be produced as a result of a shift in an activation state of the macrophages. The macrophages may shift from being M2-like macrophages to being M1-like macrophages. Optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

Further and optionally, comparing the characteristic of the immune response may involve identifying, in the quantifiable and reference immune samples, differential gene expression produced by any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, the differential gene expression may be produced as a result of a shift in an activation state of the macrophages. Further and optionally, the macrophages may shift from being M2-like macrophages to being M1-like macrophages. The macrophages may shift from being M1-like macrophages to being M2-like macrophages.

In another aspect, a method of monitoring efficacy of a treatment regime in an individual being treated for a cancer in a specific organ or tissue is provided. The method involves measuring a characteristic of an immune response in a post-treatment immune sample obtained from the specific organ or tissue after the individual has been subject to the treatment regime for a period of time, wherein the presence of a characteristic of the immune response which is greater in magnitude than would be expected had the individual not been subject to the treatment regime, is indicative of the efficacy of the treatment regime; and the treatment regime involves administering a preparation comprising one or more antigenic determinants of a microbial pathogen which is pathogenic in the corresponding specific organ or tissue in a healthy subject.

The method detailed herein may further involve measuring the characteristic of the immune response in a pre-treatment reference sample, wherein the pre-treatment reference sample was obtained from the specific organ or tissue before, at the same time as or after commencement of the treatment regime, but prior to obtaining the post-treatment immune sample, and comparing the characteristic of the immune response in the pre-treatment and post-treatment samples, wherein an increase in the magnitude of the immune response in the post-treatment immune sample compared to the pre-treatment reference sample is indicative of the efficacy of the treatment regime. Optionally, measuring the characteristic of the immune response may involve determining an indication of the number of inflammatory monocytes in a sample of the organ or tissue. Optionally, measuring the characteristic of the immune response may involve determining an indication of the number of macrophages in a sample of the organ or tissue. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages.

Optionally, measuring the characteristic of the immune response may involve determining an indication of the number of CD11b+ Gr-1+ cells in a sample of the organ or tissue or determining an indication of the number of dendritic cells in a sample of the organ or tissue. Further and optionally, measuring the characteristic of the immune response may involve determining an indication of the number of CD11c+ MHC class II+ cells in a sample of the organ or tissue or determining an indication of the number of CD4+ T cells in a sample of the organ or tissue or determining an indication of the number of CD8+ T cells in a sample of the organ or tissue.

Optionally, measuring the magnitude of the immune response may involve determining an indication of the number of NK cells in a sample of the organ or tissue. Further and optionally, comparing the characteristic of the immune response may involve identifying, in the reference and immune samples, cellular markers on any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally, the macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages.

Further and optionally, comparing the characteristic of the immune response may involve identifying, in the reference and immune samples, cytokines produced by any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. Optionally, the cytokines may be produced as a result of a shift in an activation state of the macrophages. The macrophages may shift from being M2-like macrophages to being M1-like macrophages. Further and optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response may involve identifying, in the reference and immune samples, differential gene expression produced by any one or more of the following cells as they are commonly understood to those persons skilled in the art: inflammatory monocytes, macrophages, CD11b+ Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. The macrophages may include any one or more of the following: M1-like macrophages or M2-like macrophages. The differential gene expression may be produced as a result of a shift in an activation state of the macrophages. The macrophages may shift from being M2-like macrophages to being M1-like macrophages. Optionally, the macrophages may shift from being M1-like macrophages to being M2-like macrophages.

In various aspects, embodiments of the invention relate to a method of treating a cancer situated in a lung in a subject. The method involves administering to the subject an effective amount of an antigen of one or more microbial species that is pathogenic in the lung and administering to the subject an effective amount of a platinum-containing chemotherapeutic agent. The microbial species may be a viral pathogen or a bacterial pathogen or a fungal pathogen.

As used herein, the phrase “treating a cancer” may include, without limitation, reducing the lung tumour burden in a subject or increasing life expectancy in a subject that has lung cancer. It will be understood that there are numerous biological read-outs that can be used by a person skilled in the art to determine whether a cancer is being treated or not.

The viral pathogen utilized herein may be, without limitation: influenza, adenovirus, respiratory syncytial virus, parainfluenza, monkeypox, herpes simplex virus (1 and 2), Varicella zoster, cytomegalovirus, Epstein-Barr virus, coronavirus, human metapneumovirus, Hendra virus, Nipah virus, Hantavirus, Lassa virus, human T-cell lymphotrophic virus, cocksackievirus, echovirus, enterovirus, or rhinovirus, or any virus that is pathogenic in the lung.

The bacterial pathogen utilized herein may be, without limitation: Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae, Klebsiella pneumoniae, Haemophilus influenza, Staphylococcus aureus, Chlamydia pneumoniae, Legionella pneumophila, or Bordatella pertussis or any bacterium that is pathogenic in the lung.

The fungal pathogen utilized herein may be, without limitation: Aspergillus fumigatus, Blastomyces sp., Coccidiodes immitis, Coccidiodes posadasii, Cryptococcus neoformans, Cryptococcus gattii, Fusarium sp., Histoplasma capsulatum, Paecilomyces sp., Paracoccidiodes brasiliensis, Penicillium mameffei, Pneumocystis jiroveci, Pseudallescheria boydii, Scedosporium apiospermum, Rhizopus sp., Mucor sp., Absidia sp., Cunninghamella sp., Scedosporium prolificans, Stachybotrys chartarum, Trichoderma longibrachiatium, Trichosporon sp., or any fungus that is pathogenic in the lung.

As used herein, the term “platinum-containing chemotherapeutic agent” includes, but is not limited to: Cisplatin, carboaplatin or ormaplatin, oxaliplatin, DWA2114R ((−)-(R)-2aminomethylpyrrolidine (1,1-cyclobutane dicarboxylato) platinum), zeniplatin, enloplatin, lobaplatin, CI-973 (SP-43(R)-1,1-cyclobutane-dicarboxylato(2-)-(2-methyl-1,4-65 butanediamine-N,N′)platinum), 254-S nedaplatin, JM-216 (bis-acetato-ammine-dichloro-cyclohexylamineplatinum(IV)), (see: Weiss, R. B. and Christian, M. C., “New Cisplatin Analogue in Development,” Drugs. 46:(03) 360-377 (1993)); CPA)2Pt[DOLYM] and (DACH)Pt[DOLYM] cisplatin (Choi et al., Arch. Pharmacol Res. 22(2):151-156, 1999); 254-S cisplatin analogue (Koga et al., Neurol. Res. 18(3):244-247, 1996); cis-I,4-diaminocyclohexane cisplatin analogues (Shamsuddin et al., J. Inorg. Biochem. 61(4): 291-301, 1996); MeOH cisplatin (Shamsuddin et al., Inorg. Chem. 36(25):59695971, 1997); CI-973 cisplatin analogue (Yang et al. Int. J. Oncol. 5(3):597-602, 1994); cis-diaminedichloroplatinum (II) and its analogues cis-I,1-cyclobutanedicarbosylato(2R)2-methyl-I,4-butanediamineplatinum (II) and cis-diammine (glycolato)platinum (Claycamp & Zimbrick, J. Inorg. Biochem. 26(4):257-67, 1986; Fan et al. Cancer Res. 48(11): 3135-9, 1988; Heiger-Bernays et al. Biochemistry 29(36): 8461-6, 1990; Kikkawa et al., J. Exp. Clin. Cancer Res. 12(4):233-40, 1993; Murray et al. Biochemistry 31(47):11812-17, 1992; Takahashi et al., Cancer Chemother. Pharmacol. 33(I):31-5, 1993), gem-diphosphonate cisplatin analogues (FR 2683529), cisplatin analogues containing a tethered dansyl group (Hartwig et al., J. Am. Chem. Soc. 114(21):8292-3, 1992), aminoalkylaminoanthraquinone-derived cisplatin analogues (Kitov et al., Eur. J. Med. Chem. 23(4):381-3, 1988), spiroplatin, carboplatin, iproplatin and JM40 platinum analogues (Schroyen et al., Eur. J. Cancer Clin. Oncol. 24(8): 1309-12, 1988), and JM8 and JM9 cisplatin analogues (Harstrick et al., Int. J. Androl. 10(1); 139-45, 1987).

In another aspect, use of an effective amount of an antigen of one or more microbial species that is pathogenic in the lung is provided to formulate a medicament for use with a platinum-containing chemotherapeutic agent for treating lung cancer in a subject. In another aspect, use of an effective amount of an antigen of one or more microbial species that is pathogenic in the lung is provided for use with a platinum-containing chemotherapeutic agent, as detailed herein, for treating lung cancer in a subject. The microbial species may be a viral pathogen or a bacterial pathogen or a fungal pathogen, as detailed herein.

In another aspect, an effective amount of an antigen of one or more microbial species that is pathogenic in the lung is provided to formulate a medicament for use with a platinum-containing chemotherapeutic agent for treating lung cancer in a subject. In another aspect, an effective amount of an antigen of one or more microbial species that is pathogenic in the lung is provided for use with a platinum-containing chemotherapeutic agent, as detailed herein, for treating lung cancer in a subject. The microbial species may be a viral pathogen or a bacterial pathogen or a fungal pathogen, as detailed herein. The platinum-containing chemotherapeutic agent may be, without limitation: Cisplatin, carboplatin or oxaliplatin.

In another aspect, a kit is provided. The kit includes an antigen of one or more microbial species that is pathogenic in the lung, a platinum-containing chemotherapeutic agent; and instructions for providing the antigen and the platinum-containing chemotherapeutic agent to a subject in need thereof. The microbial species may be a viral pathogen or a bacterial pathogen or a fungal pathogen, as detailed herein.

In various aspects, embodiments of the invention relate to compositions comprising components of organisms that may cause infections of the gastrointestinal tract, so that the organism may be characterized as a pathogen. However, an organism that is in some cases pathogenic may not always cause disease. Most animals are colonized to some degree by other organisms, such as bacteria, which generally exist in symbiotic or commensal relationships with the host animal. Thus, many species of normally harmless bacteria are found in healthy animals, and are usually localized to the surface of specific organs and tissues. Often, these bacteria aid in the normal functioning of the body. For example, in humans, symbiotic Escherichia coli bacteria may be found in the intestine, where they promote immunity and reduce the risk of infection with more virulent pathogens.

Bacteria that are generally harmless, such as Escherichia coli, can cause infection in healthy subjects, with results ranging from mild to severe infection to death. Whether or not an organism, such as a bacterium, is pathogenic (i.e., causes infection) depends to some extent on factors such as the route of entry and access to specific host cells, tissues, or organs; the intrinsic virulence of the bacterium; the amount of the bacteria present at the site of potential infection; or the health of the host animal. Thus, organisms that are normally harmless can become pathogenic given favorable conditions for infection, and even virulent organisms may require specific circumstances to cause infection. Accordingly, organisms that are members of the normal flora can be pathogens when they move beyond their normal ecological role in the endogenous flora. For example, endogenous species can cause infection outside of their ecological niche in regions of anatomical proximity, for example by contiguous spread. When this occurs, and in the context of the present invention, these normally harmless endogenous organisms are considered pathogenic.

Specific organisms, such as bacterial species, viruses, worms, and protozoa are known to cause infections in specific regions of the GIT in otherwise healthy subjects. Examples of organisms that commonly cause infections in specific regions of the GIT are listed below; it will be understood that these examples are not intended to be limiting and that a skilled person would be able to readily recognize and identify infectious or pathogenic organisms that cause infections, or commonly cause infections, in various regions of the GIT in healthy adults, based for example on knowledge about particular patient populations, as represented for example by the following publications: Manual of Clinical Microbiology 8th Edition, Patrick Murray, Ed., 2003, ASM Press American Society for Microbiology, Washington D.C., USA; Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases 5th Edition, G. L. Mandell, J. E. Bennett, R. Dolin, Eds., 2000, Churchill Livingstone, Philadelphia, Pa., USA, all of which are incorporated by reference herein.

Infections of the mouth are commonly caused by the following bacterial species: Prevotella melaminogenicus, anaerobic streptococci, viridans streptococci, Actinomyces spp., Peptostreptococcus spp., or Bacteroides spp., or other oral anaerobes; or viral pathogens: herpes simplex, coxsackieviruses, or Epstein-Barr.

Infections of the esophagus are commonly caused by the following bacterial species: Actinomyces spp., Mycobacterium avium, Mycobacterium tuberculosis, or Streptococcus spp.; or viral pathogens: cytomegalovirus, herpes simplex, or varicella-zoster.

Infections of the stomach are commonly caused by the following bacterial species: Streptococcus pyogenes or Helicobacter pylori; or viral pathogens: cytomegalovirus, herpes simplex, Epstein-Barr, rotaviruses, noroviruses, or adenoviruses.

Infections of the small bowel are commonly caused by the following bacterial species: Escherichia coli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, or Shigella flexneri; or viral pathogens: adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, or cytomegalovirus.

Infections of the colon/rectum are commonly caused by the following bacterial species: Escherichia coli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, or Shigella flexneri; or viral pathogens: adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, or cytomegalovirus.

Infections of the anus are commonly caused by the following bacterial species: Streptococcus pyogenes, Bacteroides spp., Fusobacterium spp., anaerobic streptococci, Clostridium spp., Escherichia coli, Enterobacter spp., Pseudomonas aeruginosa, or Treponema pallidum; or viral pathogens: herpes simplex.

Organisms such as bacteria are often classified operationally as collections of similar strains (which generally refer to groups of presumed common ancestry with identifiable physiological but usually not morphological distinctions, and which may be identified using serological techniques against bacterial surface antigens). Thus, each bacterial species (e.g., Escherichia coli) has numerous strains (or serotypes), which may differ in their ability to cause infection or differ in their ability to cause infection in a particular organ/site. Certain strains of Escherichia coli are more likely to cause gastrointestinal infection/diarrhea, including enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC), Shiga toxin-producing E. coli (STEC), enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC) and diffuse adhering E. coli (DAEC). In accordance with the present invention, one or more of an ETEC, EPEC, EHEC, STEC, EAEC, EIEC or DAEC strains of E. coli (i.e., strains that cause colon infection), may be chosen for a formulation to treat and IBD.

Similarly, there may be numerous subtypes of specific viruses, worms, or protozoa, which are associated with disease in a particular population, and are therefore amenable for use in the present invention.

The compositions of the invention include antigens of organisms that are pathogenic in a specific region of the GIT. The compositions may include the components of whole organisms, whole cells or whole virions, or may include extracts or preparations of the organisms, such as cell wall or cell membrane extracts, or exotoxins. The compositions may also include one or more isolated antigens from these organisms. Pathogenic organisms may be available commercially (for example from the American Type Culture Collection, Manassas, Va., USA), or may be clinical isolates from subjects having an infection.

The compositions of the invention derived from pathogens can be provided alone or in combination with other compounds (for example, nucleic acid molecules, small molecules, peptides, or peptide analogues), in the presence of a liposome, an adjuvant, or any pharmaceutically acceptable carrier, in a form suitable for administration to mammals, for example, humans. As used herein “pharmaceutically acceptable carrier” or “excipient” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. The carrier can be suitable for any appropriate form of administration, including subcutaneous, intradermal, intravenous, parenteral, intraperitoneal, intramuscular, sublingual, inhalational, intratumoral or oral administration. Pharmaceutically acceptable carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound (i.e., the specific bacteria, bacterial antigens, or compositions thereof of the invention), use thereof in the pharmaceutical compositions of the invention is contemplated. Supplementary active compounds can also be incorporated into the compositions.

Methods well known in the art for making formulations are found in, for example, “Remington's Pharmaceutical Sciences” (20th edition), ed. A. Gennaro, 2000, Mack Publishing Company, Easton, Pa. Formulations for parenteral administration may, for example, contain excipients, sterile water, or saline, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, or hydrogenated napthalenes. Biocompatible, biodegradable lactide polymer, lactide/glycolide copolymer, or polyoxyethylene-polyoxypropylene copolymers may be used to control the release of the compounds. Other potentially useful parenteral delivery systems for include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Formulations for inhalation may contain excipients, for example, lactose, or may be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate and deoxycholate, or may be oily solutions for administration in the form of nasal drops, or as a gel. For therapeutic or prophylactic compositions, the formulations may be administered to an individual in an amount effective to stop or slow progression of the IBD.

An “effective amount” of a pathogenic species or antigen thereof according to the invention includes a therapeutically effective amount or a prophylactically effective amount. A “therapeutically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result, such as reduction or elimination of symptoms of IBD. A therapeutically effective amount of a pathogenic species or antigen(s) thereof may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the compound to elicit a desired response in the individual. Dosage regimens may be adjusted to provide the optimum therapeutic response. A therapeutically effective amount may also be one in which any toxic or detrimental effects of the pathogenic species or antigen thereof are outweighed by the therapeutically beneficial effects. A “prophylactically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result, such as prevention of IBD. Typically, a prophylactic dose is used in subjects prior to or at an earlier stage of IBD, so that a prophylactically effective amount may be less than a therapeutically effective amount.

For administration by subcutaneous or intradermal injection, an exemplary range for therapeutically or prophylactically effective amounts of one or more pathogenic bacterial species may be about 1 million to 100,000 million organisms per ml, or may be 100 million to 7000 million organisms per ml, or may be 500 million to 6000 million organisms per ml, or may be 1000 million to 5000 million organisms per ml, or may be 2000 million to 4000 million organisms per ml, or any integer within these ranges. The total concentration of bacteria per ml may range from 1 million to 100,000 million organisms per ml, or may be 50 million to 7000 million organisms per ml, or may be 100 million to 6000 million organisms per ml, or may be 500 million to 5000 million organisms per ml, or may be 1000 million to 4000 million organisms per ml, or any integer within these ranges. The range for therapeutically or prophylactically effective amounts of antigens of a pathogenic bacterial species may be any integer from 0.1 nM-0.1 M, 0.1 nM-0.05M, 0.05 nM-15 μM or 0.01 nM-10 μM.

It is to be noted that dosage concentrations and ranges may vary with the severity of the condition to be alleviated, or may vary with the subject's immune response. In general, the goal is to achieve an adequate immune response. For administration by subcutaneous or intradermal infection, the extent of an immune response may be determined, for example, by size of delayed local immune skin reaction at the site of injection (e.g., from 0.25 inch to 4 inch diameter). The dose required to achieve an appropriate immune response may vary depending on the individual (and their immune system) and the response desired. Standardized dosages may also be used.

In the context of subcutaneous or intradermal administration, if the goal is to achieve a 2 inch local skin reaction, using a bacterial composition, the total dose may, for example, range from 2 million bacteria (e.g., 0.001 ml of a vaccine with a concentration of 2,000 million organisms per ml) to more than 20,000 million bacteria (e.g., 1 ml of a vaccine with a concentration of 20,000 million organisms per ml). The concentrations of individual bacterial species or antigens thereof within a composition may also be considered. For example, if the concentration of one particular pathogenic bacterial species, cell size of that species or antigenic load thereof is much higher relative to the other pathogenic bacterial species in the vaccine, then the local immune skin reaction of an individual may be likely due to its response to this specific bacterial species. In some embodiments, the immune system of an individual may respond more strongly to one bacterial species within a composition than another, depending for example on past history of exposure to infection by a particular species, so the dosage or composition may be adjusted accordingly for that individual.

For any particular subject, the timing and dose of treatments may be adjusted over time (e.g., timing may be daily, every other day, weekly, monthly) according to the individual need and the professional judgement of the person administering or supervising the administration of the compositions. For example, in the context of subcutaneous or intradermal administration, the compositions may be administered every second day. An initial dose of approximately 0.05 ml may be administered subcutaneously, followed by increases from 0.01-0.02 ml every second day until an adequate skin reaction is achieved at the injection site (for example, a 1 inch to 2 inch diameter delayed reaction of visible redness at the injection site). Once this adequate immune reaction is achieved, this dosing is continued as a maintenance dose. The maintenance dose may be adjusted from time to time to achieve the desired visible skin reaction (inflammation) at the injection site. Dosing may be for a dosage duration, for example of at least 2 weeks, 2 months, 6 months, 1, 2, 3, 4, or 5 years or longer.

In some embodiments, the invention may include antigenic compositions administered to one or more epithelial tissues by a non-enteric route. For example: to skin by intradermal or subcutaneous injection; to lung epithelium by inhalation. Accordingly, in some embodiments the antigenic compositions of the invention are administered so as to provoke an immune response in a non-enteric tissue, such as an epithelial tissue. In some embodiments, one or more non-enteric routes of administration may be combined with one or more additional routes of administration, such as intratumoral, intramuscular or intravenous administration.

In various aspects of the invention, the antigenic compositions that are administered to a patient may be characterized as having an antigenic signature, i.e., a combination of antigens or epitopes that is sufficiently specific that the antigenic composition is capable of eliciting an immune response that is specific to a particular pathogen, such as an adaptive immune response.

The amount of active compound (e.g., bacterial species, viruses, protozoa or helminths, or antigens thereof) in compositions of the invention may vary according to factors such as the disease state, age, sex, and weight of the individual. Dosage regimens may be adjusted to provide the optimum therapeutic response. For example, a single bolus may be administered, several divided doses may be administered over time or the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It may be advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage.

In the case of antigenic formulations (analogous to a vaccine), an immunogenically effective amount of a compound of the invention can be provided, alone or in combination with other compounds, with an immunological adjuvant. The compound may also be linked with a carrier molecule, such as bovine serum albumin or keyhole limpet hemocyanin to enhance immunogenicity. An antigenic composition (“vaccine”) is a composition that includes materials that elicit a desired immune response. An antigenic composition may select, activate or expand memory B, T cells, neutrophils, monocytes or macrophages of the immune system to, for example, reduce or eliminate the symptoms of the IBD. In some embodiments, the specific pathogenic microbe, virus, viral antigens, bacteria, bacterial antigens, or compositions thereof of the invention are capable of eliciting the desired immune response in the absence of any other agent, and may therefore be considered to be an antigenic composition. In some embodiments, an antigenic composition includes a suitable carrier, such as an adjuvant, which is an agent that acts in a non-specific manner to increase the immune response to a specific antigen, or to a group of antigens, enabling the reduction of the quantity of antigen in any given vaccine dose, or the reduction of the frequency of dosage required to generate the desired immune response. A bacterial antigenic composition may include live or dead bacteria capable of inducing an immune response against antigenic determinants normally associated with the bacteria. In some embodiments, an antigenic composition may include live bacteria that are of less virulent strains (attenuated), and therefore cause a less severe infection. In some embodiments the antigenic composition may include live, attenuated or dead viruses capable of inducing an immune response against antigenic determinants normally associated with the virus.

An antigenic composition comprising killed organisms for administration by injection may be made as follows. The organism may be grown in suitable media, and washed with physiological salt solution. The organism may then be centrifuged, resuspended in saline solution, and killed with heat. The suspensions may be standardized by direct microscopic count, mixed in required amounts, and stored in appropriate containers, which may be tested for safety, shelf life, and sterility in an approved manner. In addition to the organism and/or antigens thereof, a killed preparation suitable for administration to humans may include phenol preservative (for example 0.4%) and/or sodium chloride (for example on the order of 0.9%). The composition may also for example include trace amounts of brain heart infusion (beef), peptones, yeast extract, agar, sheep blood, dextrose, sodium phosphate and/or other media components.

In some embodiments, the antigenic composition may be used as an aerosol for inhalation.

In general, the compositions of the invention should be used without causing substantial toxicity. Toxicity of the compounds of the invention can be determined using standard techniques, for example, by testing in cell cultures or experimental animals and determining the therapeutic index, i.e., the ratio between the LD50 (the dose lethal to 50% of the population) and the LD100 (the dose lethal to 100% of the population).

In some embodiments, bacteria that are members of the endogenous flora of a particular region of the GIT may be used to formulate antigenic compositions of the invention. The rows of Table 1 list a number of bacterial species, together with the biological regions in which each species may form a part of the endogenous flora. For example, Abiotrophia spp. are typically members of the endogenous flora of the mouth.

TABLE 1 Human Bacterial Normal Flora (Endogenous Bacterial Human Pathogens) Duodenum/ Mouth Stomach Jejunum Ileum Colon CFU/mL Bacterial species 10{circumflex over ( )}5 10{circumflex over ( )}2 10{circumflex over ( )}5 10{circumflex over ( )}8 10{circumflex over ( )}11 Abiotrophia spp + Acholeplasma + laidlawii Acidaminococcus + + + + fermentans Acinetobacter + + + + spp. Actinobacillus + spp. Actinobaculum + + + + spp. Actinomyces + + + + spp. Aeromonas spp. + + + Anaerorhabdus + + furcosus Anaerococcus + + hydrogenalis Anaerococcus + + lactolyticus Anaerococcus + + prevotii Atopobium spp. + + + + Bacillus spp. + + Bacteroides + + caccae Bacteroides + + distasonis Bacteroides + + eggerthii Bacteroides + + fragilis Bacteroides + + merdae Bacteroides + + ovatus Bacteroides + + splanchnicus Bacteroides + + thetaiotaomicron Bacteroides + + vulgatus Bifidobacterium + + + adolescentis Bifidobacterium + + + bifidum Bifidobacterium + + + breve Bifidobacterium + + + catenulatum Bifidobacterium + + + + dentium Bifidobacterium + + + longum Bilophila + + + + wadsworthia Burkholderia + + + cepacia Butyrivibrio + + + fibrisolvens Campylobacter + + + concisus Campylobacter + + + curvus Campylobacter + + + gracilis Campylobacter + + + jejuni Campylobacter + + + rectus Campylobacter + + + + showae Campylobacter + sputorum Capnocytophaga + granulosum Capnocytophaga + gingivalis Campylobacter + haemolytica Capnocytophaga + + + + ochracea Capnocytophaga + sputigena Cardiobacterium + hominis Cedecea spp + Centipeda + periodontii Citrobacter + + + freundii Citrobacter + + + koseri Clostridium spp. + + + Corynebacterium + accolens Corynebacterium + afermentans Desulfomonas + + + pigra Dysgonomonas + + + spp. Eikenella + + + + corrodens Enterobacter + + + aerogenes Enterobacter + + + cloacae Enterobacter + + + gergoviae Enterobacter + + + sakazakii Enterobacter + + + taylorae Enterococcus + + + spp. Escherichia coli + + + Escherichia + + + fergusonii Escherichia + + + hermannii Escherichia + + + vulneris Eubacterium + + + + spp. Ewingella + americana Finegoldia + + + magnus Fusobacterium + alocis Fusobacterium + + + gonidiaformans Fusobacterium + + + mortiferum Fusobacterium + + + naviforme Fusobacterium + + + + necrophorum Fusobacterium + + nucleatum Fusobacterium + sulci Fusobacterium + + + russii Fusobacterium + + + varium Gardnerella + + + vaginalis Gemella + haemolysans Gemella + + + + morbillorum Globicatella spp. + + Granulicatella + spp. Haemophilus + spp. Hafnia alvei + + + Helcococcus kunzii Helicobacter spp. + + + Kingella spp. + Klebsiella spp. + + + + Lactobacillus + + + + + acidophilus Lactobacillus + breve Lactobacillus + casei Lactobacillus + + + + + fermentum Lactobacillus + + + + reuteri Lactobacillus + + + + + salivarius Leclercia + + + adecarboxylata Leminorella spp. + + + Leptotrichia + buccalis Megasphaera + + + elsdenii Micrococcus + luteus Micrococcus + lylae Micromonas + micros Mitsuokella + + + multiacidus Mobiluncus + + + curisii Mobiluncus + + + mulieris Moellerella + + + wisconsensis Moraxella + catarrhalis other Moraxella + spp. Morganella + + + morganii Mycoplasma + buccale Mycoplasma + fermentans Mycoplasma + hominis Mycoplasma + lipophilum Mycoplasma + orale Mycoplasma + pneumoniae Mycoplasma + salivarium Pantoea + + + agglomerans Pasteurella + multocida Pediococcus + + spp. Peptoniphilus + + + asaccharolyticus Peptostreptococcus + + + + anaerobus Peptostreptococcus + + + productus Porphyromonas + + + + asaccharolytica Porphyromonas + + catoniae Porphyromonas + + endodontalis Porphyromonas + + gingivalis Prevotella + + buccae Prevotella + + buccalis Prevotella + + corporis Prevotella + + dentalis Prevotella + + denticola Prevotella + + enoeca Prevotella + + heparinolytica Prevotella + + intermedia Prevotella + + loescheii Prevotella + + melaninogenica Prevotella + + nigrescens Prevotella oralis + + Prevotella oris + + Prevotella + + oulorum Prevotella + + tannerae Prevotella + + veroralis Prevotella + + zoogleoformans Propionibacterium + propionicum Proteus mirabilis + + Proteus penneri + + Proteus vulgaris + + Providencia + + rettgeri Providencia + + + stuartii Pseudomonas + + + aeruginosa Retortamonas + + + intestinalis Rothia + dentocariosa Rothia + mucilaginosa Ruminococcus + + + productus Selenomonas + spp. Serratia + + liquefaciens Serratia + + marcescens Serratia odorifera + + Staphylococcus + aureus Staphylococcus + epidermidis Streptococcus + + + agalactiae Streptococcus + + + + anginosus Streptococcus + + + bovis Streptococcus + + + + constellatus Streptococcus + criceti Streptococcus + crista Streptococcus + equisimilis Streptococcus + gordonii Streptococcus + + + intermedius Streptococcus + + mitis Streptococcus + mutans Streptococcus + oralis Streptococcus + parasanguis Streptococcus + + pyogenes Streptococcus + + salivarius Streptococcus + + sanguis Streptococcus + sobrinus Streptococcus + vestibularis Group C + G + + Streptococci Succinivibrio + + + dextrinosolvens Sutterella spp. + + + Suttonella + indologenes Tissierella + + + praeacuta Treponema + denticola Treponema + maltophilum Treponema + socranskii Treponema + vincentii Ureaplasma + urealyticum Veillonella spp. + + + +

Endogenous microbial flora, such as bacteria, have access to tissues for pathogenesis either through contiguous spread or bacteremic spread. Under favorable conditions, all endogenous organisms can become pathogenic and invade locally and spread by contiguous spread to adjacent tissues and organs. Endogenous bacterial flora of the skin, mouth and colon are the species that are understood to also be amenable to bacteremic spread. Bacteria that are members of a particular endogenous flora domain may therefore cause infection in tissues or organs to which these bacteria may spread. Accordingly, one aspect of the invention involves the use of endogenous microbial pathogens to treat an IBD having symptoms localized to a region of the GIT in which the endogenous bacteria may spread to cause infection. The columns of Table 2 list domains for endogenous flora. The rows of Table 2 list regions of the GIT within which IBD may be situated. Accordingly, one aspect of the invention involves the use of endogenous microbial pathogens to formulate antigenic compositions, or the selection of existing formulations having the pathogens, for treating an IBD situated in the region of the GIT to which the pathogen may spread to cause an infection. Accordingly, in alternative embodiments, an IBD that is symptomatic in the region listed in the first column of Table 2 may be treated with antigenic compositions comprising antigenic determinants that are specific for microbial pathogens that are members of the endogenous flora of one or more of the endogenous flora domains listed in the first row of Table 2 and indicated with an X or a check mark in the appropriate row.

TABLE 2 Tissue/Organ Pathogenicity of Endogenous Flora Tissue/organ Duo-denum/ site Mouth Stomach Jejunum Ileum Colon Oral x Tonsil x Nasopharynx/ x Sinus Esophagus x Stomach x Small bowel x x Colon/ x Rectum Anus x

In accordance with the combined information in Tables 1 and 2, IBD manifest in a particular region of the GIT set out in column 1 of Table 2 may be treated with antigenic compositions comprising antigenic determinants of the corresponding bacterial species of Table 1, so that the column headings in Table 2 are in effect replaced with the bacterial species of Table 1.

In some embodiments, pathogens for use in the invention may be exogenous bacterial pathogens. For example, the organisms listed in Table 3 may be used as microbial pathogens to formulate antigenic compositions, or antigenic compositions having those pathogens may selected, for use to treat an IBD situated in the region of the GIT listed with the relevant organism in Table 3. In some embodiments, antigenic determinants of both endogenous and exogenous bacterial species targeted to a specific tissue or organ may be used in combination. For example, an antigenic composition derived from, or specific for, Clostridium difficile, may be used to treat a IBD situated in the colon.

TABLE 3 Exogenous Bacterial Human Pathogens, and their Sites of Infection in the GIT Bacterial Species Region of the GIT Aerobacter spp. small bowel, colon, Bacillus anthracis oral, small bowel, colon, hematological Bacillus cereus colon, other Bacillus spp. colon, stomach, small bowel Brucella spp. small bowel, colon Campylobacter coli small bowel, colon Campylobacter colon jejuni Campylobacter small bowel, colon sputorum Clostridium small bowel, colon, stomach bifermentans Clostridium colon, small bowel botulinum Clostridium difficile colon Clostridium indolis small bowel, colon, stomach, Clostridium small bowel, colon, stomach mangenolii Clostridium small bowel, colon, stomach perfringens Clostridium sordellii small bowel, colon, stomach Clostridium small bowel, colon, stomach sporogenes Clostridium small bowel, colon, stomach subterminale Edwarsiella tarda small bowel, colon Francisella small bowel tularensis Helicobacter pylori stomach Leptospirosis spp. oral Listeria small bowel, colon monocytogenes Mycobacterium colon, small bowel bovis Mycobacterium small bowel, colon tuberculosis Pediococcus spp. colon Plesiomonas small bowel, colon shigelloides Rickettsia small bowel rickettsiae Salmonella spp. stomach, small bowel, colon Shigella boydii colon Shigella colon dysenteriae Shigella flexneri colon Shigella sonnei colon other Spirillum spp. colon Streptococcus small bowel zooepidemicus Treponema oral, anus pallidum Tropheryma small bowel, colon whipplei Vibrio cholerae colon, small bowel Vibrio fluvialis small bowel, colon Vibrio furnissii small bowel, colon Vibrio hollisae small bowel, colon Vibrio colon, small bowel parahaemolyticus Yersinia small bowel, colon enterocolitica Yersinia small bowel, colon pseudotuberculosis

In some embodiments, pathogens for use in the invention may be viral pathogens. Table 4 provides an exemplary list of viral pathogens together with the tissue and organ sites for which each viral species is reportedly a pathogen. Accordingly, one aspect of the invention involves utilizing immunogenic compositions that are specific for the named viruses to treat an IBD situated in the region of the GIT that is identified adjacent to the name of the virus in Table 4.

TABLE 4 Viral Human Pathogens and Their Sites of Infection Virus Region of the GIT Herpes Simplex rectum, anus virus (1 and 2) Cytomegalovirus small bowel, colon/rectum Epstein-Barr virus oral Adenovirus oral, small bowel, colon Human anus, oral papillomavirus Orthoreoviruses small bowel, colon, oral Coltiviruses oral Rotaviruses small bowel, colon Alphaviruses small bowel, colon, Coronaviruses oral, small bowel, colon Toroviruses small bowel, colon Parainfluenza oral viruses Respiratory syncytial oral virus Human oral, small bowel, colon metapneumovirus Vesicular stomatitis oral, small bowel, colon virus Rabies virus oral Influenza virus oral Hantaviruses oral Machupo virus small bowel, colon Junin virus small bowel, colon Poliovirus small bowel, colon Coxsackieviruses small bowel, colon Echoviruses oral, small bowel, colon Hepatitis A virus small bowel, colon Rhinoviruses oral Noroviruses and small bowel, colon other Caliciviruses Astroviruses small bowel, colon Picobirnaviruses small bowel, colon Hepatitis E virus small bowel, colon

The cumulative information in Tables 1 through 4 provides an extensive identification of pathogens that may be used in the formulation of antigenic compositions of the invention, together with an identification of the region of the GIT in which these organisms are pathogenic, and accordingly identifies the region of the GIT in which an IBD is situated that may be treated with an antigenic formulation of the invention. Pathogens may be selected from endogenous pathogens or exogenous pathogens.

In some embodiments, the pathogen selected for use in antigenic compositions of the invention may be one that is a common cause of acute infection in the region of the GIT in which the IBD to be treated is situated. Table 5 identifies bacterial and viral pathogens of this kind, together with the region of the GIT in which they commonly cause infection. Accordingly, in selected embodiments, an IBD residing in a region of the GIT identified in the first column of Table 5 may be treated with an antigenic composition that comprises antigenic determinants for one or more of the pathogenic organisms listed in the second column of Table 5.

TABLE 5 Common causes of acute infection (bacteria and viruses) for selected regions of the GIT Selected regions of the GIT Common Bacterial or Viral Pathogens Oral Prevotella melaninogenicus, anaerobic streptococci, viridans streptococci, Actinomyces spp., Peptostreptococcus spp., Bacteroides spp., and other oral anaerobes herpes simplex, coxsackieviruses, Epstein-Barr Stomach Streptococcus pyogenes, Helicobacter pylori cytomegalovirus, herpes simplex, Epstein-Barr, rotaviruses, noroviruses, adenoviruses Small bowel Escherichia coli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, Shigella flexneri adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, cytomegalovirus Colon/ Escherichia coli, Clostridium difficile, Bacteroides fragilis, Rectum Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, Shigella flexneri adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, cytomegalovirus Anus Streptococcus pyogenes, Bacteroides spp., Fusobacterium spp., anaerobic streptococci, Clostridium spp., E. coli, Enterobacter spp., Pseudomonas aeruginosa, Treponema pallidum herpes simplex

The specific organisms which commonly cause infection in a specific region of the GIT may vary by geographical location. Table 5 is thus not an exhaustive list of common pathogens for all geographic locations and population groups. It is understood that a clinical microbiologist skilled in the art could determine the common pathogenic species in a particular geographic area or population group for a specific region of the GIT in accordance with the invention.

Humans are hosts to a wide range of gastrointestinal parasites, including various protozoa and helminths, which for purposes of the present invention constitute pathogens of the GIT (Schafer, T. W., Skopic, A. Parasites of the small intestine. Curr Gastroenterol Reports 2006; 8:312-20; Jernigan, J., Guerrant, R. L., Pearson, R. D. Parasitic infections of the small intestine. Gut 1994; 35:289-93; Sleisenger & Fordtran's Gastrointestinal and liver disease. 8th ed. 2006; Garcia, L. S. Diagnostic medical parasitology. 5th ed. 2007). Compositions of the invention may accordingly include antigenic components of various protozoa, including for example: Giardia lamblia, Cryptosporidium parvum, Cryptosporidium hominus, Isospora belli, Sarcocystis species, Coccidian like bodies (Cyclospora species), Enterocytozoon bieneusi, Entamoeba histolytica, Entamoeba dispar, Entamoeba coli, Entamoeba hartmanni, Endolimax nana, Iodamoeba bütschlii, Dientameoba fragilis, Blastocystis hominus, Cyclospora cayetanensis, Microsporidia, Trypanosoma cruzi, Chilomastix mesnili, Pentatrichomonas hominis, Balantidium coli. Similarly, compositions of the invention may include antigenic components of various helminths, including for example: Cestodes (tapeworms), Taenia saginata, Taenia solium, Diphyllobothrium species, Hymenolepis nana, Hymenolepis diminuta, Dipylidium caninum, Nematodes (round worms), Ascaris lumbricoides, Strongyloides stercoralis, Necator americanus, Ancylostoma duodenale, Ancylostoma caninum, Tichuris trichiura, Capillaria philippinensis, Trichostrongylus species, Trichinella species, Necator americanus, Anisakis and related species, Angiostrongylus costaricensis, Enterobius vermicularis, Trematodes (flukes), Fasciolopsis buski, Heterophyes species, Echinostoma species, Clonorchis sinensis, Opisthorchis species, Fasciola species, Metagonimus yokogawi, Schistosoma mansoni, Schistosoma japonicum, Schistosoma mekongi, Schistosoma intercalatum, Echinostoma species and Paragonimus species.

In accordance with the foregoing, in various aspects, the invention may involve the treatment of an IBD with formulations of a pathogen is selected from the group consisting of: Acidaminococcus fermentans; Acinetobacter spp.; Actinobaculum spp.; Actinomyces spp.; Aeromonas spp.; Anaerorhabdus furcosus; Anaerococcus hydrogenalis; Anaerococcus lactolyticus; Anaerococcus prevotii; Atopobium spp.; Bacillus spp.; Bacteroides caccae; Bacteroides distasonis; Bacteroides eggerthii; Bacteroides fragilis; Bacteroides merdae; Bacteroides ovatus; Bacteroides splanchnicus; Bacteroides thetaiotaomicron; Bacteroides vulgatus; Bifidobacterium adolescentis; Bifidobacterium bifidum; Bifidobacterium breve; Bifidobacterium catenulatum; Bifidobacterium dentium; Bifidobacterium longum; Bilophila wadsworthia; Burkholderia cepacia; Butyrivibrio fibrisolvens; Campylobacter concisus; Campylobacter curvus; Campylobacter gracilis; Campylobacter jejuni; Campylobacter rectus; Campylobacter showae; Capnocytophaga ochracea; Cedecea spp; Citrobacter freundii; Citrobacter koseri; Clostridium spp.; Desulfomonas pigra; Dysgonomonas spp.; Eikenella corrodens; Enterobacter aerogenes; Enterobacter cloacae; Enterobacter gergoviae; Enterobacter sakazakii; Enterobacter taylorae; Enterococcus spp.; Escherichia coli; Escherichia fergusonii; Escherichia hermannii; Escherichia vulneris; Eubacterium spp.; Finegoldia magnus; Fusobacterium gonidiaformans; Fusobacterium mortiferum; Fusobacterium naviforme; Fusobacterium necrophorum; Fusobacterium nucleatum; Fusobacterium russii; Fusobacterium varium; Gardnerella vaginalis; Gemella morbillorum; Globicatella spp.; Hafnia alvei; Helicobacter spp.; Klebsiella spp.; Lactobacillus acidophilus; Lactobacillus fermentum; Lactobacillus reuteri; Lactobacillus salivarius; Leclercia adecarboxylata; Leminorella spp.; Megasphaera elsdenii; Mitsuokella multiacidus; Mobiluncus curisii; Mobiluncus mulieris; Moellerella wisconsensis; Morganella morganii; Pantoea agglomerans; Pediococcus spp.; Peptoniphilus asaccharolyticus; Peptostreptococcus anaerobus; Peptostreptococcus productus; Porphyromonas asaccharolytica; Proteus mirabilis; Proteus penneri; Proteus vulgaris; Providencia rettgeri; Providencia stuartii; Pseudomonas aeruginosa; Retortamonas intestinalis; Ruminococcus productus; Serratia liquefaciens; Serratia marcescens; Serratia odorifera; Streptococcus agalactiae; Streptococcus anginosus; Streptococcus bovis; Streptococcus constellatus; Streptococcus intermedius; Group C+G Streptococci; Succinivibrio dextrinosolvens; Sutterella spp.; Tissierella praeacuta; Veillonella spp.; Aerobacter spp.; Bacillus anthracis; Bacillus cereus; other Bacillus spp.; Borrelia recurrentis; Brucella spp.; Campylobacter coli; Campylobacter fetus; Campylobacter jejuni; Campylobacter sputorum; Clostridium bifermentans; Clostridium botulinum; Clostridium difficile; Clostridium indolis; Clostridium mangenolii; Clostridium perfringens; Clostridium sordellii; Clostridium sporogenes; Clostridium subterminale; Edwarsiella tarda; Francisella tularensis; Listeria monocytogenes; Mycobacterium bovis; Mycobacterium tuberculosis; Pediococcus spp.; Plesiomonas shigelloides; Rickettsia rickettsiae; Salmonella spp.; Shigella boydii; Shigella dysenteriae; Shigella flexneri; Shigella sonnei; other Spirillum spp.; Streptococcus zooepidemicus; Tropheryma whipplei; Vibrio cholerae; Vibrio fluvialis; Vibrio furnissii; Vibrio hollisae; Vibrio parahaemolyticus; Yersinia enterocolitica; Yersinia pseudotuberculosis; Herpes Simplex virus (1 and 2); Cytomegalovirus; Adenovirus; Orthoreoviruses; Rotaviruses; Alphaviruses; Coronaviruses; Toroviruses; Human metapneumovirus; Vesicular stomatitis virus; Machupo virus; Junin virus; Poliovirus; Coxsackieviruses; Echoviruses; Hepatitis A virus; Noroviruses and other Caliciviruses; Astroviruses; Picobirnaviruses; and Hepatitis E virus.

In alternative aspects, the invention may involve the treatment of an IBD with formulations wherein the pathogen is selected from the group of common small and larger bowel pathogens, for example the group consisting of: Escherichia coli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, Shigella flexneri; adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, and cytomegalovirus.

In selected embodiments, the invention involves diagnostic steps to assess a patient's previous exposure to an organism. For example, the diagnostic steps may include taking a medical history of exposure to selected pathogens, and/or evaluating a patient's immune response to a selected pathogen. For example, a serology test may be conducted to detect antibodies to selected pathogens in a patient's sera. In connection with this aspect of the invention, antigenic determinants of a selected pathogen may be chosen for use in an immunogenic composition on a selected patient based on a diagnostic indication that the patient has had one or more prior exposure(s) to the pathogen, for example by virtue of the presence of antibodies to antigenic determinants of that pathogen in the patient's sera.

In further selected embodiments, the invention involves diagnostic steps to assess a patient's immunological response to treatment with a selected immunogenic composition. For example, the diagnostic steps may include evaluating a patient's immune response to the antigenic determinants of that immunogenic composition, for example using a serological test to detect antibodies to those antigenic determinants. In connection with this aspect of the invention a treatment with a selected immunogenic composition may be continued if the evaluation indicates that there is an active immunological response to the antigenic determinants of that composition, and the vaccine treatment may be discontinued, and an alternative treatment with a different immunogenic composition may be initiated, if the evaluation indicates that there is not a sufficiently active immunological response to the antigenic determinants of the immunogenic composition.

Although various embodiments of the invention are disclosed herein, many adaptations and modifications may be made within the scope of the invention in accordance with the common general knowledge of those skilled in this art. Such modifications include the substitution of known equivalents for any aspect of the invention in order to achieve the same result in substantially the same way. Numeric ranges are inclusive of the numbers defining the range. The word “comprising” is used herein as an open-ended term, substantially equivalent to the phrase “including, but not limited to”, and the word “comprises” has a corresponding meaning. As used herein, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a thing” includes more than one such thing. Citation of references herein is not an admission that such references are prior art to the present invention. Any priority document(s) and all publications, including but not limited to patents and patent applications, cited in this specification are incorporated herein by reference as if each individual publication were specifically and individually indicated to be incorporated by reference herein and as though fully set forth herein. The invention includes all embodiments and variations substantially as hereinbefore described and with reference to the examples and drawings.

In some embodiments, the invention excludes steps that involve medical or surgical treatment.

The following examples illustrate embodiments of the invention.

Example 1 Clinical Studies

Bacterial Compositions

Five killed bacterial compositions have been used to treat a wide variety of cancer types and stages in blinded studies, as follows:

-   1. The Bayer Corporation MRV™ “Bayer MRV” (Hollister-Steir     Laboratories, Spokane, Wash., U.S.A.), containing the following     bacterial species:

Organisms per ml Staphylococcus aureus 1200 million  viridans and non-hemolytic Streptococci 200 million Streptococcus pneumoniae 150 million Moraxella (Neisseria) catarrhalis 150 million Klebsiella pneumoniae 150 million Haemophilus influenzae 150 million

This vaccine was produced for the following indications: rhinitis, infectious asthma, chronic sinusitis, nasal polyposis and chronic serous otitis media. Cancer treatment was not indicated as an intended use for this vaccine. The vaccine also included the following ingredients: 0.4% phenol, 0.9% NaCl, trace amounts of brain heart infusion (beef), peptones, yeast extract, agar, sheep blood, dextrose, and sodium phosphates.

-   2. Stallergenes MRV “Stallergenes MRV” (Laboratories des     Stallergenes, S. A., Fresnes, France), containing the following:

Organisms per ml Staphylococcus aureus 600 million Staphylococcus albus 600 million non-hemolytic Streptococci 200 million Streptococcus pneumoniae 150 million Moraxella (Neisseria) catarrhalis 150 million Klebsiella pneumoniae 150 million Haemophilus influenzae 150 million

This vaccine was produced for the same indications as the MRV vaccine i.e., recurrent respiratory tract infections, and listed cancer as a contraindication.

As set out below, surprisingly, these MRV vaccines, which contain many common lung pathogens, were found to be effective for the treatment of lung cancer.

-   3. Polyvaccinum Forte (PVF; Biomed S.A., Krakow, Poland), containing     the following:

Organisms per ml Staphylococcus aureus 500 million Staphylococcus epidermidis 500 million Escherichia coli 200 million Corynebacterium pseudodiphtheriticum 200 million Streptococcus pyogenes 100 million Streptococcus salivarius (viridans Streptococci) 100 million Streptococcus pneumoniae 100 million Moraxella (Neisseria) catarrhalis 100 million Klebsiella pneumoniae 100 million Haemophilus influenzae 100 million

This vaccine was produced for chronic and recurrent inflammatory conditions of the upper and lower respiratory tract and genitourinary tract, including rhinopharyngitis, recurrent laryngitis, tracheitis, bronchitis, otitis media, chronic and recurrent neuralgia of trigeminal and occipital nerve, ischialgia, brachial plexitis, intercostals neuralgia, chronic cystoureteritis, vaginitis, adnexitis, and endometrium inflammation. Cancer treatment was not indicated as an intended use for this vaccine.

Of note, although the total concentration of bacteria in PVF is identical to that of the MRVs (Bayer and Stallergenes), patients typically demonstrated a visible inflammatory immune response to subcutaneous injection of the PVF composition at a much smaller dose than the usual dose required to achieve a similar skin response with the MRV composition, indicating that the immune reaction was likely occurring to one of the novel components in the Polyvaccinum Forte vaccine, such as E. coli. As set out below, surprisingly, PVF, which contains E. coli a common pathogen of the colon, abdomen, kidney, ovaries, peritoneum, liver and pancreas, has been found to be effective in the treatment of cancers in the colon, abdominal lymph nodes, kidney, ovary, peritoneum, liver and pancreas.

-   4. Staphage Lysate (Delmont Laboratories Inc., Swarthmore, Pa.,     USA), containing the following:     Staphylococcus aureus

As set out below, surprisingly, Staphage Lysate, which contains Staphylococcus aureus a common pathogen of the breast and bone, was found to be effective in the treatment of cancer in the breast and bone.

Administration of MRV, Staphage Lysate and PVF

The bacterial compositions (vaccines) were a suspension of killed bacterial cells and therefore, the suspensions were gently shaken prior to use to ensure uniform distribution prior to withdrawing dose from vial, and administered subcutaneously three times a week on Mondays, Wednesdays, and Fridays. Patients were advised to continue treatment for at least 6 months. The dose of vaccine required was determined by the adequacy of the immune reaction to the vaccine. Beginning with a very small dose (0.05 cc), the dose was gradually increased (by 0.01-0.02 cc each time) until an adequate immune reaction was achieved. This delayed local reaction at the injection site appeared within 2-48 hours after injection and lasted for up to 72 hours or longer. The goal was to achieve a one to two inch diameter round patch of pinkness/redness at the injection site, indicating adequate immune stimulation. Once this reaction was achieved, the dose was maintained at the level required to achieve this reaction. If the reaction was significantly less than two inches (e.g., half an inch) the dose was increased, if it was significantly more than two inches (e.g., three inches), the dose was decreased. This local immune reaction generally occurs within the first 24 hours after the injection. Patients were asked to check for this reaction and, if present, to measure or mark it. The maintenance dose required to achieve an adequate immune reaction varies considerably, depending on the individual's immune response—as little as 0.001 cc for some people, as much as 2 cc for others. The vaccine must be stored in a refrigerator (2° to 8° C.). The usual site for injection is the upper arms, the thighs or the abdomen. The exact site of each injection was varied so that it was not given in sites in which pinkness/redness was still present. A known contraindication to the vaccines is hypersensitivity to any component of the vaccine.

A fifth vaccine, a polymicrobial oral vaccine, was used in alternative aspects of the invention, as follows:

-   5. Respivax, produced by BB-NCIPD Ltd (Bulgaria). This oral vaccine     contained the following freeze-dried killed bacterial species:

Organisms per mg Streptococcus pneumoniae 25 million Neisseria catarrhalis 25 million Streptococcus pyogenes 25 million Haemophilus influenzae 25 million Staphylococcus aureus 25 million Klebsiella pneumoniae 25 million Administration of Respivax

The Respivax oral vaccine was produced for the treatment for chronic respiratory infection, and contains many of the most common respiratory tract pathogens, including many of the most common causes of lung infection. Patients were treated with a dose of one 50 mg tablet per day, providing the equivalent of 1.25×10⁹ cells of each species per dose. Patients were prescribed the above dose for a continuous period of at least 6 months.

As set out below, surprisingly, Respivax oral vaccine, which contains many common lung pathogens, was found to be effective for the treatment of cancer of the lung.

Example 1A Cancer of the Lung

This section relates to primary cancer in the lung, or metastases to the lung, treated with microbial pathogens of the lung, such as endogenous respiratory bacteria flora.

Patients qualified for the lung cancer study if they were initially diagnosed with stage 3B or 4-lung (inoperable) cancer. Lung cancer staging was performed using standard methods as for example described in AJCC: Cancer Staging Handbook (sixth edition) 2002; Springer-Verlag New York: Editors: Fredrick Greene, David Page and Irvin Fleming, or in International Union Against Cancer: TNM Classification of Malignant Tumors (sixth edition) 2002; Wiley-Liss Geneva Switzerland: Editors: L. H. Sobin and C. H. Wittekind. For example, lung cancers may be classified as follows:

TNM Lung Clinical and Pathological Classification

T Primary Tumour

-   TX Primary tumour cannot be assessed, or tumour proven by the     presence of malignant cells in sputum or bronchial washings but not     visualized by imaging or bronchoscopy -   Tis Carcinoma in situ -   T0 No evidence of primary tumour -   T1 Tumour 3 cm or less in greatest dimension, surrounded by lung or     visceral pleura, without bronchoscopic evidence of invasion more     proximal than the lobar bronchus (ie, not in the main bronchus) -   T2 Tumour with any of the following features of size or extent: More     than 3 cm in greatest dimension Involves main bronchus, 2 cm or more     distal to the carina Invades visceral pleura Associated with     atelectasis or obstructive pneumonitis that extends to the hilar     region but does not involve the entire lung

T3 Tumour of any size that directly invades any of the following: chest wall (including superior sulcus tumours), diaphragm, mediastinal pleura, parietal pericardium; or tumour in the main bronchus less than 2 cm distal to the carina but without involvement of the carina; or associated atelectasis or obstructive pneumonitis of the entire lung

-   T4 Tumour of any size that invades any of the following:     mediastinum, heart, great vessels, trachea, esophagus, vertebral     body, carina; or tumour with a malignant pleural or pericardial     effusion; or with separate tumour nodule(s) within the ipsilateral     primary-tumour lobe of the lung     N Regional Lymph Nodes -   NX Regional lymph nodes cannot be assessed -   N0 No regional lymph node metastasis -   N1 Metastasis in ipsilateral peribronchial and/or ipsilateral hilar     lymph nodes and intrapulmonary nodes, including involvement by     direct extension -   N2 Metastasis in ipsilateral mediastinal and/or subcarinal lymph     node(s) -   N3 Metastasis in contralateral mediastinal, contralateral hilar,     ipsilateral or contralateral scalene, or supraclavicular lymph     node(s)     M Distant Metastasis -   MX Distant metastasis cannot be assessed -   M0 No distant metastasis -   M1 Distant metastasis; includes separate tumour nodule(s) in the     non-primary-tumour lobe (ipsilateral or contralateral)     Stacie Grouping of TNM Subsets:

Occult TX N0 M0 carcinoma Stage 0 Tis N0 M0 Stage IA T1 N0 M0 Stage IB T2 N0 M0 Stage IIA T1 N1 M0 Stage IIB T2 N1 M0 T3 N0 M0 Stage IIIA T3 N1 M0 T1 N2 M0 T2 N2 M0 T3 N2 M0 Stage IIIB Any T N3 M0 T4 Any N M0 Stage IV Any T Any N M1

Charts with diagnostic codes 162.9 (lung cancer) and 197 (metastatic cancer) were collected manually and electronically. Information was collected on these patients, such as date of diagnosis, date of death, and cancer stage. Charts for patients were reviewed to confirm the date of diagnosis and cancer stage. Patients were excluded from the analysis for the following reasons: 1) wrong stage; 2) missing data; 3) no chart, or; 4) chart did not reach in time for the data analysis. 20 patients were excluded from the study because their charts have not arrived yet or there was insufficient information, of which 6 were MRV users. The study group includes 108 patients in total: 50 who took the MRV vaccine and 58 who did not take the MRV vaccine.

Comparison of survival of patients initially diagnosed with stage 3B and 4 lung cancer who took MRV with patients who didn't take MRV and with SEER standard survival data for patients initially diagnosed with stage 3B and 4 lung cancer (FIG. 1) was as follows:

SEER non-MRV MRV median survival: 5 months 10.5 months 12.5 months survival at 1 year: 25% 45% 58% survival at 5% 3% 20% 3 years: survival at 3% 0% 10% 5 years:

A comparison of survival (as above), including only those patients who took MRV for at least 2 months (FIG. 2) is as follows:

-   median survival: 16.5 months -   survival at 1 year: 70% -   survival at 3 years: 27% -   survival at 5 years: 15%

Median survival and survival at 1 year, 3 years and 5 years, was substantially better in the group that was treated with MRV (containing bacteria which commonly cause lung infection), evidence of the effectiveness of this vaccine for the treatment of lung cancer. Patients who were treated with the MRV vaccine for more than 2 months had higher survival rates, further evidence of the effectiveness of this vaccine for the treatment of lung cancer.

An alternative analysis was conducted on data that included a patient population to whom the MRV composition was not available, to address a perceived potential for bias caused by sicker patients being more likely to choose the novel treatment (with MRV) and healthier patients being potentially less likely to submit to the use of the antigenic compositions of the invention. Comparison of survival of MRV patients to whom the MRV composition was available (designated “Lung 1”) to survival of non-MRV patients to whom the MRV composition was not available (designated “Lung 2”) removes some of this selection bias, providing a clearer and more accurate illustration of the benefit of MRV treatment, as illustrated in FIG. 3.

In some embodiments, particularly striking clinical benefits have been obtained with antigenic bacterial compositions used in repeated frequent injections (i.e., three times per week) for a prolonged period of time—such as at least 2, 3, 4, 5, 6 or 12 months, or 2, 3, 4 or 5 years (in the context of advanced cancer such as inoperable lung cancer, the longer periods may be most beneficial). Treatments of this kind may be carried out so as to provide sustained, prolonged immune stimulation. When the above analysis is restricted to patients who were treated with MRV for a minimum of 2 months, the survival advantage of MRV treatment is even more clearly illustrated FIG. 4.

As illustrated in FIG. 4, one-year survival of stage 3B or 4 lung cancer patients treated with MRV for at least two months was 70%, compared to just 48% for the non-MRV Lung 2 group and 23% for the SEER database group. 3-year survival of the MRV group was more than 4 times that of both the non-MRV patients and the SEER registry. None of the non-MRV group in the Lung 2 study survived for 5 years, whereas 15% of patients treated with MRV for a minimum two-month period were still alive 5 years after diagnosis. In the context of an illness such as inoperable lung cancer that is considered terminal and has a usual 5-year survival rate of only 3% (SEER registry), the above results are extremely encouraging and surprising.

When the analysis of patient data is restricted to patients who were treated with MRV for at least 6 months, the survival curve is truly remarkable, as illustrated in FIG. 5. More than 60% of patients were alive at 3 years, more than 10 times the survival in both the non-MRV group and the SEER registry. 36% (5 of 14 patients) of patients who were treated with MRV for at least 6 months were alive 5 years after diagnosis, compared with only 3% in the SEER database and 0% in the non-MRV group. These remarkable results, in the context of a cancer diagnosis that is considered terminal, are extremely promising and surprising. Accordingly, in some embodiments, cancers, such as advanced cancers, such as inoperable lung cancer, may be treated over a dosing duration of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 months, 2 years, 3 years, 4 years, 5 years, or indefinitely.

Restricting analysis to those patients who were treated with MRV for a minimum period of time (e.g., 6 months) introduces a bias in favour of the MRV group, since MRV patients who survived for less than that period of time are excluded from the group (including those who died before they could complete the 6 months of treatment). A detailed statistical analysis of this bias, with compensatory exclusion of short-term survivors in both the non-MRV and SEER groups, demonstrates that this bias played a very minor role in the truly remarkable survival advantage of patients who were treated with the MRV for at least 6 months.

In stage 3B lung cancer, cancer is confined to the lungs, and thus, a targeted anti-cancer treatment response may be stimulated, in accordance with various aspects of the invention, by a vaccine, such as MRV, comprised of lung pathogens. In stage 4 lung cancer, the cancer has metastasized to distant organs not amenable to targeted stimulation by lung pathogens in accordance with methods of the invention. Thus, in accordance with some embodiments, patients with stage 3B lung cancer may be selected for treatment with MRV vaccine, since all of the cancer is confined to the lungs and thus, will be targeted by the MRV vaccine. When the analysis of patient data is restricted to patients with stage 3B lung cancer, comparison of survival curves even more clearly illustrates the benefit of MRV treatment. As illustrated in FIG. 11, one-year survival of stage 3B lung cancer patients treated with MRV was 76%, compared to just 53% for the non-MRV Lung 2 group and 23% for the SEER database group. 3-year survival of the MRV group was 3 times that the non-MRV patients and more than 6 times the SEER registry. None of the non-MRV group survived for 5 years, whereas 14% of stage 3B patients treated with MRV were still alive 5 years after diagnosis. In the context of an illness such as inoperable stage 3B lung cancer that is considered terminal and has a usual 5-year survival rate of only 5% (SEER registry), the above results are extremely encouraging and surprising.

As some patients did not have their first visit for many months or even a year or two after diagnosis, their inclusion in the survival curves skews the curve towards longer survival. In order to determine whether this bias influenced the difference in survival curves, survival was analysed from date of first visit which excludes this bias, as illustrated in FIG. 12. Comparison of survival curves of stage 3B lung cancer patients in FIG. 12 demonstrates an even greater survival benefit for MRV treatment than illustrated in FIG. 11, indicating that the benefit of MRV treatment was partially masked in FIG. 11. As illustrated in FIG. 12, 1-year survival (from date of first visit) of stage 3B lung cancer patients treated with MRV was 57%, compared to only 21% for stage 3B patients not treated with MRV. While no stage 3B lung cancer patients not treated with MRV survived for 3 years, 3-year survival of stage 3B patients treated with MRV was 33% and 5-year survival was 14%, a remarkable and unexpected result.

When analysis was restricted to stage 3B lung cancer patients whose first visit was within 3 months of diagnosis, the benefits of early treatment with MRV are clearly illustrated. As illustrated in FIG. 13, while all stage 3B lung cancer patients who had their first visit within 3 months of diagnosis died within 1 year of diagnosis, 70% of stage 3B lung cancer patients treated with MRV within 3 months of diagnosis survived for 1 year, 40% survived 3 years and 20% survived 5 years, a truly remarkable survival benefit for early MRV treatment.

One aspect of the invention involves the treatment of primary lung cancers or metastasis to the lung with antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be lung pathogens, such as exogenous lung pathogens or pathogens that are members of the endogenous flora of the respiratory system. For example, antigenic determinants of the endogenous bacterial respiratory flora species that most commonly cause infection in the lung (see Table 5) may be used to treat primary and metastatic cancers situated in the lung: Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae, Klebsiella pneumoniae, Haemophilus influenza. Similarly, common viral lung pathogens from Table 5 may be selected for use in some embodiments. Alternatively, a more exhaustive list of endogenous lung pathogens may be selected from Table 1, based on the pathogenicity information provided in Table 2. In further alternative embodiments, viral lung pathogens listed in Table 4 may be used. And in further alternative embodiments, exogenous bacterial lung pathogens from Table 3 may be used in formulating antigenic compositions of the invention, i.e. selected from the group consisting of: Achromobacter spp., Actinomadura spp., Alcaligenes spp., Anaplasma spp., Bacillus anthracis, other Bacillus spp., Balneatrix spp., Bartonella henselae, Bergeyella zoohelcum, Bordetella holmesii, Bordetella parapertussis, Bordetella pertussis, Borrelia burgdorferi, Borrelia recurrentis, Brucella spp., Burkholderia gladioli, Burkholderia mallei, Burkholderia pseudomallei, Campylobacter fetus, Capnoctyophaga canimorsus, Capnoctyophaga cynodegmi, Chlamydia pneumoniae, Chlamydia psittaci, Chlamydophila pneumoniae, Chromobacterium violaceum, Chlamydophila psittaci, Chryseobacterium spp., Corynebacterium pseudotuberculosis, Coxiella bumetii, Francisella tularensis, Gordonia spp., Legionella spp., Leptospirosis spp., Mycobacterium avium, Mycobacterium kansasii, Mycobacterium tuberculosis, other Mycobacterium spp., Nocardia spp., Orientia tsutsugamushi, Pandoraea spp., Pseudomonas aeruginosa, other Pseudomonas spp., Rhodococcus spp., Rickettsia conorii, Rickettsia prowazekii, Rickettsia rickettsiae, Rickettsia typhi.

For example, since the MRV compositions contain many of the most common lung pathogens, these vaccines may be used to treat primary lung cancer or lung metastases, as illustrated in the cumulative data presented here, and in a number of the case reports. In accordance with the foregoing results, one aspect of the invention involves the treatment of primary lung cancer and metastasis to the lung with antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be pathogenic in the lung, such as exogenous lung pathogens or pathogens that are members of the endogenous flora of the respiratory tract. In selected embodiments, antigenic determinants of the common lung pathogens may be used to treat primary and metastatic cancers situated in the lung, for example, antigenic determinants from one or more of the following bacterial species or viral types: Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae, Klebsiella pneumoniae, Haemophilus influenza, influenza virus, adenovirus, respiratory syncytial virus, and parainfluenza. In further selected embodiments, antigenic determinants of Streptococcus pneumoniae, the most common cause of bacterial lung infection, may be used alone or with other of the most common pathogens of the lung to treat cancer of the lung.

Primary lung cancer may also arise from bronchial tissue and therefore, in some embodiments, antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to cause bronchial infection may be used to treat patients with cancer situated in the bronchial tissue, including, for example, the following common causes of bronchial infection: Mycoplasma pneumoniae, Chlamydophila pneumoniae, Bordetella pertussis, Streptococcus pneumoniae, Haemophilus influenzae, influenza virus, adenovirus, rhinovirus, coronavirus, parainfluenza, respiratory syncytial virus, human metapneumovirus, or coxsackievirus. Lung cancer (or lung metastases) that is located in both lung and bronchial tissue may be treated with antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to cause both lung and bronchial infection (for example, Streptococcus pneumoniae, Haemophilus influenza and Mycoplasma pneumoniae are all common lung and bronchial pathogens) or alternatively, with antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to cause lung infection and antigenic determinants of microbial pathogens that are known to cause bronchial infection.

Example 1B Breast Cancer with Metastasis to the Bone or Lung

The most common cause of both breast infection and bone infection is Staphylococcus aureus. Accordingly, in one aspect of the invention, an antigenic composition comprising antigenic determinants of S. aureus may be used to treat breast cancer with metastases to the bone. The remarkable case of Patient R (PtR), treated with a Staphylococcus aureus vaccine, set out below in the Case Reports, illustrates the efficacy of this approach to treating breast cancer with bone metastases. As illustrated in FIG. 6, in a cumulative series of 52 patients, survival of breast cancer patients with metastases to bone and/or lung treated with MRV (n=19), which contains Staphylococcus aureus, was better than the survival of patients not treated with the MRV vaccine (n=33):

% survival MRV patients % survival non-MRV patients 10 months 95% 76% 20 months 74% 61%  5 years 26% 18%

In accordance with the foregoing results, one aspect of the invention involves the treatment of primary cancer in the breast or metastasis to the breast with antigenic compositions that comprise antigenic determinants of microbes that are known to cause breast infection, and treatment of primary cancer of the bone or metastasis to the bone with antigenic compositions that comprise antigenic determinants of bacterial species or viruses that are known to cause bone infection. In selected embodiments, a vaccine comprising antigenic determinants of Staphylococcus aureus, the most common cause of both breast and bone infection, may be used alone or in combination with other of the most common pathogens of the breast to treat cancer in the breast, or alone or in combination with other of the most common pathogens of the bone to treat cancer in the bone.

Example 1C Metastases to the Bone

One of the most common sites for metastases in patients with prostate cancer is bone. In one aspect of the invention, the MRV composition, which contains antigenic determinants of S. aureus, the most common cause of bone infection, may be used for the treatment of metastases to the bone, for example in patients who have, or who have had, a primary prostate cancer. The graph of FIG. 7 is a comparison of survival of a cumulative series of metastatic prostate cancer patients who had surgery or radiation to destroy their prostate gland (and thus, the primary tumour) and who had detectable cancer limited to bone metastases. As illustrated, the survival of patients treated with MRV (n=4) is substantially better than that of patients not treated with MRV (n=7):

% survival MRV patients % survival non-MRV patients 2 years 100% 57% 3 years  75% 43% 5 years  50%  0%

In accordance with the foregoing results, one aspect of the invention involves the treatment of primary bone cancers or metastases to the bone with antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to cause bone infection, such as exogenous bone pathogens or pathogens that are members of the endogenous flora of the skin, mouth or colon. For example, in selected embodiments, antigenic determinants of one or more of the following microbial species from the list of common bone pathogens may be used to treat primary and metastatic cancers situated in the bone: Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus agalactiae, other streptococci spp., Escherichia coli, Pseudomonas spp., Enterobacter spp., Proteus spp., Serratia spp., parvovirus B19, rubella, hepatitis B. In further selected embodiments, Staphylococcus aureus, the most common cause of bone infection, may be used alone or with other of the most common pathogens of the bone to treat cancer of the bone.

Example 1D Cancer Situated in the Colon

Treatment with the PVF composition has been shown to improve the survival of colon cancer patients (see FIG. 8), as illustrated by a comparison of the following four colon cancer patient groups:

-   -   Stage 4 colon cancer patients who were treated with MRV.     -   Stage 4 colon cancer patients who were not treated with a         vaccine.     -   Stage 4 colon cancer patients who were treated with PVF vaccine.     -   Stage 4 colon cancer patients from the SEER (Surveillance,         Epidemiology and End Results) database.

This example illustrates that patients with colon cancer treated with PVF, which contains E. coli the most common cause of bacterial infection of the colon, have substantially improved survival.

Patients qualified for the first two groups of this study if they presented with stage 4 colon cancer. Patients were excluded from this analysis for the following reasons:

-   -   incorrect diagnosis     -   incorrect stage     -   missing essential data (e.g., date of death)     -   no chart     -   chart did not reach us in time for the data analysis.

The patient group included a total of 136 stage 4 colon cancer patients: 15 who took the PVF vaccine, 56 who took the MRV vaccine, and 65 who did not take a vaccine. Results are illustrated in FIG. 8, as follows:

SEER no vaccine MRV PVF median survival: 8.4 mo. 15.1 mo. 15.0 mo. 33.6 mo. at 10 months 45% 69% 71% 100% at 20 months 24% 42% 36%  67% at 30 months 14% 29% 23%  52% at 5 years  5%  6%  7%  10%

The median survival of patients with stage 4 colon cancer treated with PVF (which contains E. coli, one of the most common colonic pathogens) was more than double that of patients treated with MRV (which does not contain colonic pathogens) or patients not treated with a vaccine, and four times that of the SEER registry. All 15 patients treated with PVF were still alive 10 months after diagnosis, compared to only 71% for the MRV group, 69% for the no-vaccine group and only 45% for the SEER registry. Survival at 30 months for the PVF group was double that of both the MRV group and the no-vaccine group and almost 4 times that of the SEER registry.

The wilcoxon test shows a statistically significant survival difference between patients treated with PVF vaccine and both the MRV group (p=0.0246) and the no vaccine group (p=0.0433). This is remarkable considering the small size of the PVF group (n=15), indicative of substantial therapeutic effect. As evidenced by these results, the PVF composition, which contains E. coli the most common cause of bacterial infection of the colon, is an effective treatment for colon cancer.

Survival of those patients who presented for immunological treatment in accordance with the invention within 3 months of diagnosis (i.e., excluding those patients who were long-term survivors before presenting for treatment) has also been analyzed. The results of this analysis are presented in FIG. 9. As illustrated, the ‘MRV’ and ‘No Vaccine’ survival curves in FIG. 9 are shifted substantially to the left (indicating that a selection bias towards ‘long-term’ survivors may have artifactually shifted these curves to the right in FIG. 8), whereas, remarkably, the PVF curve in FIG. 9 is actually further to the right than the curve in FIG. 8, indicating that the benefit of earlier treatment with PVF (i.e., within 3 months of diagnosis) more than outweighed any long-term survivor bias excluded in FIG. 9. This analysis provides compelling evidence that the benefit of PVF treatment for stage 4 colon cancer may be even greater than that illustrated in FIG. 8, and that the earlier the treatment with the compositions of the invention is begun following diagnosis, the greater the benefit.

In accordance with the foregoing results, one aspect of the invention involves the treatment of colon cancers with antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be colon pathogens, such as pathogens that are members of the endogenous flora of the colon or exogenous colonic pathogens. For example, antigenic determinants of the following microbial species may be used to treat primary and metastatic cancers situated in the colon: Escherichia coli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, Shigella flexneri; adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, or cytomegalovirus. For example, cancers situated in the colon may be treated with the PVF composition, which contains E. coli, or alternative formulations that include only antigenic determinants of colonic pathogens. In selected embodiments, antigenic determinants of E. coli, the most common bacterial cause of colon infection, may be used alone or with antigenic determinants of other common pathogens of the colon to treat cancer of the colon.

Example 1E Use of Respivax, an Oral Vaccine to Treat Lung Cancer

Oral Respivax vaccine was administered as described above, with a dose of one 50 mg tablet per day, providing the equivalent of 1.25×10⁹ cells of each species per dose. Patients were advised to continue the above dose for at least 6 months.

As illustrated in FIG. 10, survival of stage 3B lung cancer patients who were treated with the oral Respivax antigens was substantially better than patients who were not treated with the antigenic composition. Median survival was 37 months for the patients treated with Respivax, compared to only 20 months for those patients not treated with an antigenic composition vaccine. 40% of patients treated with Respivax were alive 5 years after diagnosis, whereas none of the untreated patients survived for more than 2 years.

In accordance with the foregoing results, one aspect of the invention involves the treatment of primary of the lung or metastases to the lung with oral administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that commonly cause lung infection.

Example 2 Case Reports

These case reports are indicative of the patients that make up the patient populations reflected in the foregoing cumulative studies, as well as illustrating additional aspects of the invention. In particular, the individual case reports of Patients A-N are illustrative of surprising results in some patients being treated with anti-inflammatories, while the case reports of Patients O-AA are representative of the general patient population that includes many examples of vaccine treatment that was effective in the absence of anti-inflammatory therapy.

MRV for Cancer of the Lung with and without Anti-Inflammatories

Patient A (PtA): In September year 0, PtA developed right upper chest pain with an associated wheeze. These symptoms persisted and in January, year 1, she had a chest x-ray that revealed a large 7 cm×8 cm mass in the apex of the right lung. A fine needle aspiration was positive for non-small cell lung cancer. On January 27, year 1, an MRI showed invasion of the subclavian arteries, making surgical resection impossible and thus, PtA was diagnosed with stage 3B inoperable terminal lung cancer. She underwent a short course of palliative radiation and declined chemotherapy. She was told that she had terminal cancer with a 3 to 6 months life expectancy.

On April 29, year 1, PtA began therapy with MRV vaccine three times per week. On that same date she also began treatment with the non-steroidal anti-inflammatory agent (NSAID) indomethicin 50 mg four times per day and a regime of antioxidant supplements and vitamin D. 18 months later, by October, year 2, the tumour had markedly reduced in size to 3 cm in diameter and, by May 19, year 5, four years after starting treatment with the combined regime of MRV vaccine, indomethicin, antioxidants vitamins and vitamin D, only residual scarring remained. PtA continued treatment with this combination of MRV vaccine and adjuvant anti-inflammatory therapies for more than 4 years until the end of May, year 5 at which time there was no evidence of residual cancer, in spite of a diagnosis of terminal inoperable lung cancer more than 4 years previously. More than 14 years since diagnosis with terminal lung cancer, PtA continues to feel well with no evidence of residual cancer.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancers in the lung with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that commonly cause lung infection.

In accordance with the forgoing results, another aspect of the invention involves the administration of the immunogenic compositions repeatedly relatively frequently over a relatively long period of time.

The concomitant use of anti-inflammatory agents, such as antioxidants, vitamin D and indomethicin, in conjunction with targeted MRV therapy, was associated with substantially improved survival, which was greater than that of otherwise similar cases, in which these adjuvant anti-inflammatory modalities were not used in conjunction with the compositions of the invention. For example, Patient B, an otherwise similar case in which anti-inflammatories were not administered, was diagnosed with inoperable stage 3B non-small cell lung cancer, which was fatal within 3 months of diagnosis. These cases provide evidence of a synergistic effect between the antigenic compositions of the invention and anti-inflammatory treatments.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancers with both the administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are pathogenic to the organ or tissue targeted, as well as adjuvant anti-inflammatory treatments, for synergistic effect.

MRV for Cancer of the Lung with and without Anti-Inflammatories

Patient C (PtC): In the spring of year 0, PtC began having pain in his right upper chest area. This pain persisted and on October 5, year 0 he had a chest x-ray that revealed a large 12 cm×11 cm mass occupying virtually the entire right upper lobe. A fine needle aspiration was positive for poorly differentiated non-small cell lung cancer. Exploratory thoracotomy was performed on December 7, year 0, which revealed tumour invasion of the chest wall and superior vena cava and therefore, PtC's tumour was inoperable (i.e., stage 3B). PtC underwent a short course of palliative radiation and declined chemotherapy. He was told that he had terminal cancer with a 3 to 6 months life expectancy. By January 27, year 1, the rapidly growing tumour had increased in size to 14 cm×11.5 cm.

On February 9, year 1, PtC began treatment with indomethicin 50 mg four times per day, antioxidant vitamins, and vitamin D. Three weeks later, on March 1, year 1, PtC began treatment with MRV vaccine three times per week. By June, year 1, PtC was feeling well and was running 8 km 3-4 times per week. On June 4, year 1, a chest x-ray revealed that the tumour had reduced in size to 11 cm diameter. PtC continued to feel very well, leading a full and active life with return to full employment and continued full physical activity. PtC continued treatment with a combination of the MRV vaccine and adjuvant anti-inflammatory therapies (indomethicin, antioxidants and vitamin D) for more than 16 months until July 24, year 2, at which time indomethicin treatment was discontinued (as a result of decreased kidney function, a known potential side-effect of long-term indomethicin use). 6 months later, in December, year 2, after 22 months of targeted vaccine therapy, MRV treatment was discontinued (since MRV was no longer available past that date). PtC continued to feel well until June, year 6, at which time he was diagnosed with a recurrence of cancer in both lungs, which lead to his death on May 26, year 7, more than 6.5 years after he was diagnosed with terminal lung cancer and told he had 3-6 months to live.

In this case, the use of adjuvant anti-inflammatory agents, including antioxidants, vitamin D and indomethicin, used in conjunction with targeted MRV therapy for more than 16 months, was associated with substantially improved survival in the face of a diagnosis that is usually fatal within 1 year, which was greater than that of an otherwise similar case, Patient D, in which these adjuvant anti-inflammatory modalities were not used in conjunction with the compositions of the invention, and an inoperable lung cancer was fatal within 8 months of diagnosis. These cases provide evidence of a synergistic effect between the antigenic compositions of the invention and anti-inflammatory treatments.

PVF for Cancer of the Colon with Metastases to the Liver and Lung, and without Anti-Inflammatories

Patient E (PtE): PtE had a surgical resection of colon cancer on June 17, year 0, followed by chemotherapy. On August 15, year 0, he was diagnosed stage 4 cancer with metastases to the liver and lungs, a diagnosis with a very poor prognosis. On October 20, year 0, PtE began treatment with an antioxidant and vitamin D regime and, on December 10, year 0, he began treatment with the PVF composition three times per week, which he has continued in combination with the antioxidants and vitamin D. In September, year 1, he began treatment with Celebrex™ 100 mg twice per day. In spite of a very poor initial prognosis, PtE was still and feeling well at last contact, more than 3 years after diagnosis with terminal metastatic colon cancer.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancers of the colon, liver and lung with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be pathogenic in the colon, liver and lung.

In contrast to PtE, of the 15 patients diagnosed with stage 4 colon cancer and treated with PVF, the patient with the shortest survival, Patient F, was not treated with anti-inflammatories. These cases provide compelling evidence that anti-inflammatory modalities (i.e., Celebrex™, anti-oxidants and vitamin D) taken in conjunction with targeted PVF therapy has a synergistic effect, contributing to PtE's prolonged survival, which was greater than that of otherwise similar cases in which these adjuvant anti-inflammatory modalities were not used in conjunction with the compositions of the invention.

PVF for Cancer of the Colon with Metastases to Lung, with Anti-Inflammatories

Patient G (PtG): PtG developed rectal bleeding in May, year 0, and was diagnosed with colon cancer. He underwent surgery, chemotherapy and radiation, but developed metastases to his lungs (stage 4 cancer) on 16 August, year 1, a terminal diagnosis with a poor prognosis. He had begun a regime of antioxidant vitamins and vitamin D in June, year 0, and, on September 23, year 1, he began taking the NSAID Celebrex 100 mg twice per day. In March, year 3, he began PVF vaccine three times per week, which he continued till April, year 4 at which time he developed brain metastases, which lead to his death on June 2, year 4, almost 3 years after a diagnosis of stage 4 terminal colon cancer. PtG lived substantially longer than would normally be expected with a diagnosis of stage 4 colon cancer with metastases to the lungs. In this context, the invention provides for the use of anti-inflammatory modalities in conjunction with immunogenic compositions, such as PVF, for synergistic effect.

Patient H (PtH): PtH was diagnosed with colon cancer with metastases to the liver and lungs on February 13, year 0. On January 11, year 1, he was prescribed an antioxidant and vitamin D regime. However, in March, year 1, he entered a chemotherapy research study and discontinued these supplements at that time at the request of the study coordinators. He was not treated with any NSAIDs. On May 12, year 1, he began treatment with PVF, which he took three times per week until his death just 2.5 months later. When contrasted to similar cases that involved the use of anti-inflammatories, this case illustrates that, if adjuvant anti-inflammatory modalities are not given concomitantly with the targeted antigenic activation therapy, there is a lack of a synergistic effect that would otherwise occur with concomitant use of adjuvant anti-inflammatory modalities.

In summary, in cases of stage 4 colon cancer treated with targeted PVF vaccine therapy, the use of adjuvant anti-inflammatory agents, including antioxidants, vitamin D and Celebrex, used in conjunction with targeted antigenic activation therapy, was associated with substantially improved survival, much greater than that of the two cases in which these adjuvant anti-inflammatory modalities were not used in conjunction with the vaccine, providing evidence suggestive of a synergistic effect.

PVF with and without Anti-Inflammatories for Cancer of the Pancreas with Metastases to the Lungs, Liver and Abdominal Lymph Nodes

Patient I (PtI): PtI was diagnosed with pancreatic cancer in August, year 1, at which time he had surgery to remove his pancreas (i.e., Whipple's procedure). However, in July year 2, he developed metastases to the lungs bilaterally and in February year 4 he developed recurrence of cancer in the pancreatic area with abdominal and liver metastases. This is a terminal diagnosis with a very poor prognosis. PtI began a regime of antioxidant vitamins, vitamin D, large doses of turmeric (curcumin), fish oil (9 gm per day), resveratrol and green tea (equivalent of 36 cups per day) on September 27, year 2, all of which are anti-inflammatory modalities, all of which he continued to take. In March year 3, he began treatment with Celebrex 100 mg twice per day, which he took for more than 20 months. PtI began treatment with PVF three times per week in May year 4, which he has continued to use regularly for more than 3 years. PtI survived for 5 years after a diagnosis of terminal metastatic pancreatic cancer, a remarkably prolonged survival in the context of a diagnosis that has an extremely poor prognosis. This case provides evidence that high doses of multiple anti-inflammatory modalities (i.e., Celebrex, antioxidants, vitamin D, turmeric, fish oil, resveratrol, green tea) taken in conjunction with the PVF compositions, resulted in a synergistic effect which has contributed to PtI's remarkable survival for 5 years after developing metastatic pancreatic cancer, a diagnosis that is usually fatal within 6 months.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancer of the pancreas, abdominal lymph nodes, liver and lung with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to cause infection in the pancreas, abdominal lymph nodes, liver and lungs.

Patient J (PtJ) had an essentially identical diagnosis to PtI (i.e., pancreatic cancer with metastases to abdominal lymph nodes, lungs and liver). PtJ, who did not take any other anti-inflammatories along with the PVF vaccine except antioxidants and vitamin D, died within 4 months of diagnosis, whereas PtI, who took large doses of numerous other anti-inflammatories modalities (i.e., Celebrex, turmeric, fish oil, resveratrol and green tea) in conjunction with PVF vaccine, survived for 5 years after diagnosis. These cases provide evidence of a synergistic effect of high dose multiple anti-inflammatory modalities and targeted vaccine therapy.

MRV for Cancer of the Breast with Metastases to the Bone

Patient K (PtK): In March, year 0, PtK developed neck and back pain, which persisted. On July 28, year 0, she was diagnosed with stage 4 breast cancer with metastases to the cervical spine, an incurable diagnosis. She underwent surgery to remove two breast lumps (axillary lymph nodes positive) and palliative radiation to the metastases in her spine. On January 18, year 1, PtK began treatment with doses of antioxidants and vitamin D, as well as the NSAID indomethicin 50 mg four times per day. Three days later, on January 21, year 1, she began treatment with the MRV composition, which contains Staphylococcus aureus the most common pathogen of both the breast and bone. Although there was no documentation of the exact length of time that treatment with this combination of MRV/indomethicin/antioxidant/vitamin D was continued, the patient was given sufficient vaccine (20 ml) for approximately 2 years of treatment at the usual dose and frequency (i.e., three times per week) and PtK stated that she completed the recommended treatment course at home. Remarkably, PtK was still alive at last contact, 13 years after diagnosis with stage 4 metastatic breast cancer with metastases to bone.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancers of the breast and bone with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be pathogenic in the breast and bone infection.

In contrast to Patient K, Patient L (PtL) was diagnosed with breast cancer with metastases to bone on October 11, year 0. She was not prescribed an NSAID or other anti-inflammatories. PtL began treatment with MRV on February 27, year 1. She died 9 months later on November 4, year 1, just over one year after diagnosis with stage 4 breast cancer with metastases to bone. The contrast between the otherwise similar cases of PtK and PtL illustrates the potential for synergistic treatment with anti-inflammatories and the antigenic compositions of the invention.

MRV with and without Anti-Inflammatories for Cancer of the Breast with Metastases to the Bone

Patient M (PtM): PtM was diagnosed with stage 4 breast cancer with metastases to bone on June 15, year 0. She began on the NSAID Naprosyn 250 mg twice per day on an ongoing basis for pain relief and, in October, year 3, she began doses of antioxidants and vitamin D. Three months later, on January 15, year 4, she began treatment with MRV vaccine (which contains Staphylococcus aureus, the most common breast and bone pathogen) in combination with these anti-inflammatory therapies (i.e., Naprosyn, antioxidants and vitamin D). PtM lived for more than 9 years after being first diagnosed with stage 4 metastatic breast cancer with metastases to bone, an unusually long survival considering the usual poor prognosis associated with this diagnosis.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancers of the breast and bone with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be common causes of breast and bone infection.

In contrast to PtM, Patient N (PtN): PtN was diagnosed with stage 4 cancer with metastases to bone on April 8, year 0. She began doses of antioxidants and vitamin D on April 24, year 0. However, prior to starting MRV, she was prescribed the blood thinner warfarin, limiting supplementation with vitamin E and vitamin C, two important antioxidants that can lead to potential complications if used in conjunction with warfarin. In addition, NSAIDs could not be prescribed in this case since they are contraindicated with warfarin use. On June 2, year 1 PtN began treatment with MRV. She died 14 months later in August, year 2. In this context, it is possible that the use of targeted vaccine therapy without the synergistic effect of adjuvant anti-inflammatories (i.e., NSAID, vitamin E and therapeutic doses of vitamin C) limited its potential benefit.

In summary, in the cases of stage 4 breast cancer with metastases to the bone treated with targeted MRV therapy detailed above, the use of adjuvant anti-inflammatory agents in conjunction with MRV was associated with substantially improved survival, much greater than that of the two cases in which these adjuvant anti-inflammatory modalities were not used in conjunction with the vaccine, providing evidence suggestive of a synergistic effect.

MRV for Metastases to the Lungs

Patient O (PtO) was diagnosed in June, year 0 with kidney cancer with metastases to the lungs bilaterally and to the bone (left femur). This is generally considered to be an incurable terminal diagnosis with a poor prognosis. He began treatment with the MRV on August 10, year 0 and continued regular treatment (three times per week) for 16 months (after which MRV was no longer available). In September, year 0, he began 7 months of treatment with an experimental drug, pegylated interferon alpha-2a. His left femur was ‘pinned’ due to the risk of fracture as a result of the metastasis but, due to surgical complications, amputation of the left leg below the mid-thigh was required. In September, year 2, his cancerous right kidney was removed. In October, year 2, a PET scan found no evidence of cancer in the lungs and no further evidence of bone metastases. PtO is alive with no evidence of cancer in his lungs, more than 9 years after a diagnosis of bilateral pulmonary metastases, a remarkable result.

In accordance with the foregoing results, one aspect of the invention involves the treatment of metastases to the lung with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be lung pathogens.

MRV for Metastases to the Bone and Lungs

Patient P (PtP) was diagnosed with kidney cancer in July, year 0, and underwent excision of this right kidney. In December, year 4, he developed metastases to the bone (femurs bilaterally) and lungs (bilaterally). PtP declined conventional treatment and began treatment with MRV in April, year 5, which he continued regularly, three times per week, for 18 months. PtP's health improved and he returned to normal daily activities. X-rays and imaging of the chest and femurs showed no progression, with stable disease in the lungs and femurs during the 18 months that PtP was on MRV treatment.

In accordance with the foregoing results, one aspect of the invention involves the treatment of metastases to the lung and bone with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are common causes of lung and bone infection.

MRV for Metastases to the Lungs

Patient Q (PtQ) was diagnosed with colon cancer with probable metastases to the lungs in June, year 0. At that time, the primary colon tumour was fully excised, leaving only several lung metastases. PtQ started treatment with MRV on Dec. 11, year 0 which she continued three times per week for 4 months. On April 19, year 1, after 6 months treatment with chemotherapy, she had surgery to excise the only visible lung lesion remaining, which was confirmed to be a metastatic lesion. A diagnosis of colon cancer with lung metastases has a poor prognosis, even in the context of chemotherapy followed by surgery to excise visible metastases. In spite of her original poor prognosis, PtQ remains in excellent health, with no evidence of cancer more than 10 years after her initial diagnosis with metastases to the lung and treatment with MRV.

S. aureus Antigens for Breast Cancer with Metastasis to the Bone

Patient R (PtR): In May, year 0, PtR was diagnosed with breast cancer with metastases to her sternum, femur and cervical spine, an incurable cancer with a poor prognosis. She was treated with radiation and Tamoxefen. In May, year 4, she developed an additional area of metastasis in her lumbar spine and she began on treatment with Megace. In November, year 4, she began treatment with a vaccine (Staphage Lystate vaccine) containing only Staphylococcus aureus, the most common cause of infection of both the breast and bone and thus, a selected formulation for the treatment of breast and bone cancer. She continued regular therapy with this vaccine for 5 years. In spite of a diagnosis of metastatic breast cancer with multiple bone metastases, PtR survived for more than 17 years, a remarkable survival in the context of incurable metastatic breast cancer and a testament to the promise of targeted vaccine therapy for the treatment of breast cancer.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancers of the breast and bone with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be the most common cause of the breast and bone infection.

This embodiment illustrates that a formulation that includes antigenic determinants of only the most frequently pathogenic organism or organisms for a tissue may provide particular advantages, as is also illustrated in the mouse model data set out below. In keeping with this, we have found enhanced effectiveness of Respivax as opposed to MRV in treating cancers situated in the lung, reflecting the fact that the Respivax formulation is somewhat more optimal because it includes higher relative concentrations of the pathogenic species which most commonly cause lung infection (i.e., 67% of the bacterial cell count of Respivax is comprised of species that most commonly cause lung infection, whereas only 30% of the MRV vaccines are comprised of species that most commonly cause lung infection).

In accordance with the foregoing results, one aspect of the invention involves formulating the antigenic compositions such that antigenic determinants of microbial pathogens that are known to be the common causes of infection are given preferential priority in the proportions of the formulation, with the most common cause of infection receiving the greatest preferential priority. For example, the proportion of antigenic determinants that are derived from pathogens that are known to be a common cause of infection may be 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100%.

Accordingly, in some embodiments, the invention provides antigenic compositions in which a threshold proportion of antigenic determinants selected in accordance with the invention are used, relative to any other antigenic determinants in the composition. For example, antigenic compositions may have greater than X % of the antigenic determinants therein derived from pathogenic (or commonly pathogenic, or most commonly pathogenic) species, where X may for example be 10, 20, 30, 40, 50, 60, 70, 80, 90, 95 or 100 (or any integer value between 10 and 100). For example, at least X % of the antigenic determinants in the antigenic composition may be specific for microbial pathogens that are pathogenic (or commonly pathogenic, or most commonly pathogenic) in the specific organ or tissue of the patient within which the cancer is situated. Using an alternative measure, of the total number of microbial pathogens in the antigenic composition, at least X % may be selected to be microbial pathogens that are pathogenic (or commonly pathogenic, or most commonly pathogenic) in the specific organ or tissue of the patient within which the cancer is situated. In some embodiments, the antigenic composition may accordingly consist essentially of antigenic determinants of one or more microbial pathogens that are each pathogenic in the specific organ or tissue within which the cancer is situated. In selected embodiments, the antigenic composition may consist essentially or entirely of antigenic determinants of microbial pathogens that are commonly pathogenic in the specific organ or tissue of the patients with which the cancer is situated. In further selected embodiments, the antigenic antigenic composition may consist essentially or entirely of antigenic determinants of a microbial pathogen (or pathogens) that are most commonly pathogenic in the specific organ or tissue of the patients with which the cancer is situated.

In the context of various aspects of the invention, organisms are characterized by the frequency with which they are pathogenic. In this context, the invention also relates to the frequency with which endogenous flora are pathogenic. For clarity, in this regard, the characterizations herein of the frequency of pathogenicity, such as the designation “commonly pathogenic” relate, in general, to the proportion of infections in a particular organ or tissue that are commonly attributed to a particular organism, and not to the frequency with which microbial colonization of a tissue is converted to a pathogenic infection. In North America, the majority of human infections are understood to be caused by endogenous organisms, even though these organisms commonly are present as part of the endogenous flora without causing infection. For example, while S. pneumonia is a common cause of lung infection (i.e., pneumonia) in humans (and thus, is designated “commonly pathogenic” in the lung), it is nevertheless also true that S. pneumoniae is commonly present as part of the endogenous flora of the respiratory tract without causing infection and thus, in the nature of an endogenous colonization, is not normally pathogenic.

MRV for Multiple Myeloma

Patient S (PtS) was diagnosed with multiple myeloma (stage 3A) in the fall of year 0, with multiple lesions on bone scan, including skull, humeri and pelvis. He was treated with standard chemotherapy (melphalan and prednisone) for 6 months. However, in December year 3, he developed a pathological fracture of his right femur as a result of his disease, which required pinning and local radiation. On April 28, year 4, PtS began treatment with MRV, which contains Staphylococcus aureus a common cause of septicemia, which he continued for more than 13 years until this vaccine was no longer available in December year 17. Remarkably, PtS is still alive almost 25 years after being diagnosed with multiple myeloma, a truly extraordinary outcome considering his ‘terminal’ diagnosis.

In accordance with the foregoing results, one aspect of the invention involves the treatment of hematological cancers with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to cause septicemia.

In accordance with the forgoing results, and as illustrated in other patient case reports detailed herein, another aspect of the invention involves the administration of the immunogenic compositions repeatedly relatively frequently over a relatively long period of time, as described elsewhere herein.

PVF for Colon Cancer with Metastases of the Liver and Abdominal Lymph Nodes

Patient T (PtT) was diagnosed with colon cancer and was treated with excision of the primary tumour (and subsequent chemotherapy) in September year 0. Ten months later, she developed a liver metastasis, which was surgically excised in July year 1. PtT remained well until June year 7, when she was diagnosed with recurrent disease—an inoperable mass of abdominal lymph nodes in close proximity to the aorta and spine, obstructing her left ureter, requiring insertion of a nephrostomy tube. PtT was considered terminal and treated with palliative radiation in October year 7. She began treatment with PVF on November 17, year 7, which she continued every second day. PtT survived for almost 4 years after being diagnosed with terminal recurrent metastatic colon cancer.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancer in abdominal lymph nodes with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to cause infection in abdominal lymph nodes.

MRV for Metastasis to the Skin and Perineum

Patient U (PtU) was diagnosed with colon cancer and was treated with excision of the primary tumour in November year 0. He was diagnosed with stage 4 cancer in July year 2 with metastases to the perineum (i.e., peri-anal/genital soft tissue area) and skin. He had further surgery to remove as much of the cancer as possible in the perineum (cancer extended past surgical margins) with follow-up radiation and chemotherapy. The only known cancer sites remaining were in the skin and perineum. PtU started treatment with MRV, which contains Staphylococcus aureus a common cause of skin and perineal infection, on May 25, year 3, which he continued three times per week for 5 months. In spite of his original poor prognosis, PtU is in excellent health more than 10 years after his diagnosis with stage 4 cancer with metastases to the perineum and skin.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancer of the skin and perineum with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be common causes infection in the skin and perineum.

PVF for Metastases to the Peritoneum

Patient V (PtV) was diagnosed with breast cancer in May, year 0, at which time she had a mastectomy with adjuvant chemotherapy. In January, year 12, she developed abdominal pain and ascites and was diagnosed with peritoneal metastases, a diagnosis with a poor prognosis. On August 5, year 12, PtV began treatment with PVF, which contains E. coli a common cause of peritoneal infection, which she continued regularly for 1 year. Her tumour markers and ascites decreased and, in August year 13, after one year of PVF treatment, she had abdominal surgery for an unrelated medical condition, at which time the surgeon could not find any evidence of the previous peritoneal cancer. PtV discontinued use of the vaccine. PtV was still alive at last contact, 3 years and 9 months after being diagnosed with terminal peritoneal metastases.

In accordance with the foregoing results, one aspect of the invention involves the treatment of peritoneal metastases with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to cause peritoneal infection.

PVF for Ovarian and Pelvic Cancer

Patient W (PtW) was diagnosed with stage 3B poorly differentiated ovarian cancer in the fall of year 0. She had surgery in November year 0, with removal of the left ovary, but the cancer could not be completely excised and thus, she was at extreme risk for recurrence. She had a full course of post-operative chemotherapy. However, in year 2 her tumour markers began to rise and in January year 3 she was diagnosed with a recurrence in her right ovary area. She had surgery to remove this right ovarian mass in February year 3, but again the cancer could not be completely excised and she had follow-up chemotherapy. However, once again in December year 3 she developed a further recurrence in the pelvic area and retroperitoneal lymphadenopathy. She began treatment with PVF vaccine, which contains E. coli a cause of ovarian and pelvic infection, on January 5, year 4, which she continued for 6 months. Her tumour markers, which had risen to 2600, fell to the 300 range. PtW was alive and feeling very well at last contact, 2 years and 9 months after being diagnosed with recurrent ovarian cancer. Of note is the fall in her tumour markers following PVF treatment.

In accordance with the foregoing results, one aspect of the invention involves the treatment of ovarian and pelvic cancer with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to cause infection in the ovary and pelvic areas.

MRV for Follicular Non-Hodgkin's Lymphoma

Patient Y (PtY): was diagnosed with stage 4A Follicular Non-Hodgkin's lymphoma, with extensive marked lymphadenopathy (i.e., enlarged lymph glands). He declined all conventional treatment. PtY began treatment with the MRV composition, which contains many of the pathogens which commonly cause infection of the lymph nodes of the head and neck, axillae, mediastinum and inguinal areas. In addition, he began treatment with a multiple vitamin/supplement regime, healthful diet and other immune enhancement treatments. He continued regular use of this vaccine for more than 3 years, at which time his lymph glands had begun to greatly reduce in size and he was feeling well. This resolution of lymphadenopathy continued, and imaging showed almost complete resolution of previous extensive lymphadenopathy. PtY was feeling well and there was no lymphadenopathy palpable: a clearly remarkable recovery. Five years after his initial diagnosis with Stage 4A Follicular Non-Hodgkin's lymphoma, PtY had no evidence of recurrence and was leading an active and healthy life. Treatment with MRV vaccine resulted in complete remission of his stage 4A follicular non-Hodgkins' lymphoma.

In accordance with the foregoing results, one aspect of the invention involves the treatment of lymphoma with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be common causes of lymph node infection in the region the lymphoma is located.

PVF for Colon Cancer with Metastases to the Liver and Kidneys

Patient Z (PtZ) was diagnosed with metastatic spread of previously treated colon cancer, with a metastasis to the liver and probable other metastases to both kidneys. The liver metastasis was excised. The prognosis for this stage (i.e., stage 4) of colon cancer is poor and the benefit of further conventional treatment (i.e., chemotherapy) is limited. PtZ declined chemotherapy initially. Three months after diagnosis with metastatic colon cancer, PtZ began treatment with Polyvaccinum Forte (PVF), which contains E. coli, a common cause of infection of the colon, liver and kidneys. In addition PtZ began treatment with a multiple vitamin/supplement regime and healthful diet. He continued regular use of this vaccine and the vitamin and supplement regime, and began chemotherapy. Although the overall course of his disease was slowly progressive, with development of lung metastases and recurrence of liver metastases, 28 months after his initial diagnosis of metastatic disease, his weight was stable and his energy levels were good. Three years (36 months) after diagnosis of stage 4 colon cancer, PtZ was feeling well except for nausea and mild weight loss related to chemotherapy.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancer of the colon, liver and kidneys with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be pathogenic in the colon, liver and kidneys.

PVF for Colon Cancer with Metastases to the Liver, Porta Hepatic Lymph Nodes and Lung

Patient AA (PtAA) was diagnosed with metastatic colon cancer with metastases to the liver, portahepatic lymph nodes and lungs. The prognosis for this stage (i.e., stage 4) of colon cancer is very poor (i.e., ‘terminal’ cancer) and the benefit of conventional treatment (i.e., chemotherapy) is limited. PtAA began chemotherapy, but discontinued treatment approximately 5 months after his diagnosis due to side effects, at which time he began treatment with Polyvaccinum Forte (containing bacterial species which cause infection in the colon, liver, abdominal lymph nodes and lungs) every second day as well as a multiple vitamin/supplement regime and a healthy diet. PtAA's subsequent CT Scans demonstrated necrotic porta hepatic lymph nodes unchanged in size from the time of his diagnosis and no change in size of the lung metastases, although the two liver metastases grew moderately in size (3.4 cm to 4.5 cm and 1.2 cm to 3.0 cm). In spite of the very poor prognosis, PtAA continued to feel quite well almost one year after a diagnosis of terminal cancer.

In accordance with the foregoing results, one aspect of the invention involves the treatment of cancer of the colon, liver, abdominal lymph nodes and lungs with administration of antigenic compositions that comprise antigenic determinants of microbial pathogens that are known to be pathogenic in the colon, liver, abdominal lymph nodes and lungs.

Example 3 Microbial Pathogens

In alternative aspects, the invention utilizes microbial antigens, such as bacterial or viral antigens, to formulate antigenic compositions, where the microbial species is selected on the basis of the tissue or organ within which the microbe is known to cause infections. Bacterial resident flora are the most common bacterial pathogens, accounting for the vast majority of bacterial infections in most animals, including humans. Resident flora can for example infect through primary attachment, or attachment and invasion following mucosa damage, resulting for example from vascular, trauma, chemical insult, or damage resulting from primary infection.

For microbial pathogens, virulence and infection potential is a combination of the ability of the microbe to adhere, to produce enzymes, to survive immunoproducts (complement, antibody) and to survive the microbiocidal activity of macrophage and neutrophils. Some bacteria, including endogenous bacteria, may be sufficiently virulent as to cause monomicrobial infections, while others are more effective with the synergy of polymicrobial infection. In general, it is often not possible to be precise about the specific role of individual microbes within the milieu of mixed infection. As acute infection may, in some cases, provide more optimal immune stimulation, accordingly, in some embodiments, the invention utilizes microbial species that are involved in acute infection.

In some embodiments, bacteria that are members of the endogenous flora of a particular region may be used to formulate antigenic compositions of the invention. The rows of Table 6 list a number of bacterial species, together with the biological regions in which each species may form a part of the endogenous flora. For example, Abiotrophia spp. are typically members of the endogenous flora of the respiratory tract and the mouth. Further and for example, the organisms listed in Table 6 may be used as microbial pathogens to formulate antigenic compositions, or antigenic compositions having those pathogens may be selected, for use to treat inflammatory conditions, cancers, for example as an anti-inflammatory treatment for cancers, inflammation associated with cancers, or inflammatory conditions situated in the tissues or organs listed with the relevant organism in Table 6.

TABLE 6 Human Bacterial Normal Flora (Endogenous Bacterial Human Pathogens) Duodenum/ GU Bacterial species Respiratory Mouth Stomach Jejunum Ileum Colon System Genital Skin CFU/mL 10{circumflex over ( )}5 10{circumflex over ( )}2 10{circumflex over ( )}5 10{circumflex over ( )}8 10{circumflex over ( )}11 Abiotrophia + + spp Acholeplasma + + laidlawii Acidaminococcus + + + + + fermentans Acinetobacter + + + + + + + + spp. Actinobacillus + + spp. Actinobaculum + + + + + spp. Actinomyces + + + + + + + spp. Aerococcus + christensenii Aerococcus + viridans Aerococcus + urinae Aeromonas + + + spp. Alloiococcus + otitis Anaerorhabdus + + furcosus Anaerococcus + + + + hydrogenalis Anaerococcus + + + lactolyticus Anaerococcus + + + prevotii Arcanobacterium + + spp. Atopobium + + + + + spp. Bacillus + + + spp. Bacteroides + + caccae Bacteroides + + distasonis Bacteroides + + eggerthii Bacteroides + + + + fragilis Bacteroides + + merdae Bacteroides + + ovatus Bacteroides + + splanchnicus Bacteroides + + thetaiotaomicron Bacteroides + + vulgatus Bifidobacterium + + + adolescentis Bifidobacterium + + + + + bifidum Bifidobacterium + + + + + breve Bifidobacterium + + + + + catenulatum Bifidobacterium + + + + + + + dentium Bifidobacterium + + + + + longum Bilophila + + + + + + + wadsworthia Brevibacterium + casei Brevibacterium + epidermidis Burkholderia + + + + cepacia Butyrivibrio + + + fibrisolvens Campylobacter + + + + concisus Campylobacter + + + + curvus Campylobacter + + + + gracilis Campylobacter + + + jejuni Campylobacter + + + rectus Campylobacter + + + + + showae Campylobacter + + sputorum Capnocytophaga + + granulosum Capnocytophaga + + gingivalis Campylobacter + + haemolytica Capnocytophaga + + + + + + + ochracea Capnocytophaga + + sputigena Cardiobacterium + + hominis Cedecea + spp Centipeda + + periodontii Citrobacter + + + freundii Citrobacter + + + koseri Clostridium + + + spp. Corynebacterium + + + accolens Corynebacterium + + + afermentans Corynebacterium + amycolatum Corynebacterium + auris Corynebacterium + + diphtheriae Corynebacterium + durum Corynebacterium + glucuronolyticum Corynebacterium + jeikeium Corynebacterium + macginleyi Corynebacterium + matruchotii Corynebacterium + minutissimum Corynebacterium + propinquum Corynebacterium + pseudodiphtheriticum Corynebacterium + riegelii Corynebacterium + simulans Corynebacterium + + striatum Corynebacterium + ulcerans Corynebacterium + + urealyticum Dermabacter + hominis Dermacoccus + nishinomiyaensis Desulfomonas + + + pigra Dysgonomonas + + + spp. Eikenella + + + + + corrodens Enterobacter + + + aerogenes Enterobacter + + + cloacae Enterobacter + + + gergoviae Enterobacter + + + sakazakii Enterobacter + + + taylorae Enterococcus + + + spp. Escherichia + + + + + coli Escherichia + + + fergusonii Escherichia + + + hermannii Escherichia + + + vulneris Eubacterium + + + + + spp. Ewingella + + americana Finegoldia + + + + + magnus Fusobacterium + + alocis Fusobacterium + + + + + gonidiaformans Fusobacterium + + + mortiferum Fusobacterium + + + + + naviforme Fusobacterium + + + + + necrophorum Fusobacterium + + + nucleatum Fusobacterium + + sulci Fusobacterium + + + russii Fusobacterium + + + varium Gardnerella + + + + + vaginalis Gemella + + haemolysans Gemella + + + + + morbillorum Globicatella + + spp. Granulicatella + + spp. Haemophilus + + + spp. Hafnia alvei + + + Helcococcus + kunzii Helicobacter + + + spp. Kingella + + spp. Klebsiella + + + + + spp. Kocuria + spp. Kytococcus + sedentarius Lactobacillus + + + + + + + + acidophilus Lactobacillus + + breve Lactobacillus + + + + casei Lactobacillus + + cellobiosus Lactobacillus + + + + + + + + fermentum Lactobacillus + + + + reuteri Lactobacillus + + + + + + salivarius Lactococcus + + spp. Leclercia + + + adecarboxylata Leminorella + + + spp. Leptotrichia + + + + buccalis Leuconostoc + + spp. Megasphaera + + + elsdenii Micrococcus + + + luteus Micrococcus + + + lylae Micromonas + + micros Mitsuokella + + + multiacidus Mobiluncus + + + + curisii Mobiluncus + + + + mulieris Moellerella + + + wisconsensis Moraxella + + catarrhalis other + + + + Moraxella spp. Morganella + + + morganii Mycoplasma + + buccale Mycoplasma + faucium Mycoplasma + + + fermentans Mycoplasma + + genitalium Mycoplasma + + + hominis Mycoplasma + + lipophilum Mycoplasma + + orale Mycoplasma + penetrans Mycoplasma + + pneumoniae Mycoplasma + primatum Mycoplasma + + salivarium Mycoplasma + spermatophilum Neisseria + cinerea Neisseria + flavescens Neisseria + lactamica Neisseria + + meningitidis Neisseria + mucosa Neisseria + polysaccharea Neisseria + sicca Neisseria + subflava Oligella + + ureolytica Oligella + + urethralis Pantoea + + + agglomerans Pastuerella + + bettyae Pasteurella + + multocida Pediococcus + + spp. Peptococcus + + + niger Peptoniphilus + + + + + + asaccharolyticus Peptoniphilus + lacrimalis Peptostreptococcus + + + + + anaerobus Peptostreptococcus + + + productus Peptostreptococcus + + + vaginalis Porphyromonas + + + + + + asaccharolytica Porphyromonas + + + catoniae Porphyromonas + + + endodontalis Porphyromonas + + + gingivalis Prevotella + + bivia Prevotella + + + buccae Prevotella + + + + + buccalis Prevotella + + + corporis Prevotella + + + dentalis Prevotella + + + denticola Prevotella + + disiens Prevotella + + + enoeca Prevotella + + + heparinolytica Prevotella + + + intermedia Prevotella + + + + + loescheii Prevotella + + + + + melaninogenica Prevotella + + + nigrescens Prevotella + + + + + oralis Prevotella + + + oris Prevotella + + + oulorum Prevotella + + + tannerae Prevotella + + + + + veroralis Prevotella + + + zoogleoformans Propionibacterium + acnes Propionibacterium + avidum Propionibacterium + granulosum Propionibacterium + + propionicum Propionfera × + innocuum Proteus + + + mirabilis Proteus + + + penneri Proteus + + + vulgaris Providencia + + rettgeri Providencia + + + stuartii Pseudomonas + + + aeruginosa Retortamonas + + + intestinalis Rothia + + dentocariosa Rothia + + mucilaginosa Ruminococcus + + + productus Selenomonas + + spp. Serratia + + liquefaciens Serratia + + marcescens Serratia + + odorifera Staphylococcus + + + + + aureus Staphylococcus + auricularis Staphylococcus + capitis Staphylococcus + caprae Staphylococcus + cohnii Staphylococcus + + + + + epidermidis Staphylococcus + haemolyticus Staphylococcus + hominis Staphylococcus + lugdunensis Staphylococcus + pasteuri Staphylococcus + saccharolyticus Staphylococcus + + saprophyticus Staphylococcus + schleiferia Staphylococcus + simulans Staphylococcus + xylosus Staphylococcus + warneri Streptococcus + + + + + agalactiae Streptococcus + + + + + + + anginosus Streptococcus + + + bovis Streptococcus + + + + + + + constellatus Streptococcus + + criceti Streptococcus + + crista Streptococcus + + equisimilis Streptococcus + + gordonii Streptococcus + + + + + + intermedius Streptococcus + + + mitis Streptococcus + + mutans Streptococcus + + oralis Streptococcus + + parasanguis Streptococcus + pneumoniae Streptococcus + + + + pyogenes Streptococcus + + + salivarius Streptococcus + + + sanguis Streptococcus + + sobrinus Streptococcus + + vestibularis Group C + G + + Streptococci Succinivibrio + + + dextrinosolvens Sutterella + + + + + spp. Suttonella + + indologenes Tissierella + + + praeacuta Treponema + + denticola Treponema + + maltophilum Treponema + minutum Treponema + phagedenis Treponema + refringens Treponema + + socranskii Treponema + + vincentii Turicella + otitidis Ureaplasma + + + urealyticum Veillonella + + + + + spp. Weeksella + + virosa

Endogenous microbial flora, such as bacteria, have access to tissues for pathogenesis either through contiguous spread or bacteremic spread. Under favorable conditions, all endogenous organisms can become pathogenic and invade locally and spread by contiguous spread to adjacent tissues and organs. Endogenous bacterial flora of the skin, mouth and colon are the species that are understood to also be amenable to bacteremic spread. Bacteria that are members of a particular endogenous flora domain may therefore cause infection in tissues or organs to which these bacteria may spread. Accordingly, one aspect of the invention involves the use of endogenous microbial pathogens to treat a cancer of a tissue or organ to which the endogenous bacteria may spread to cause infection. The columns of Table 7 list 9 domains for endogenous flora, the: skin, respiratory system, genitals, GU system, mouth, stomach, duodenum/jejunum, ileum and colon. The rows of Table 7 list organs or tissues within which cancers may be situated. Accordingly, one aspect of the invention involves the use of endogenous microbial pathogens to formulate antigenic compositions, or the selection of existing formulations having the pathogens, for treating cancers situated in tissues or organs to which the pathogen may spread to cause an infection. Accordingly, in alternative embodiments, tumors situated in the tissues or organs listed in the first column of Table 7 may be treated with antigenic compositions comprising antigenic determinants that are specific for microbial pathogens that are members of the endogenous flora of one or more of the endogenous flora domains listed in the first row of Table 7 and indicated with an X or a check mark in the appropriate row. For example, tumors situated in the prostate may be treated with an antigenic composition having antigenic determinants specific for a microbial pathogen or pathogens endogenous to the GU system and/or genital system. A number of the bacterial species that are endogenous to the endogenous flora domains listed in Table 7 are listed, with the corresponding endogenous flora domains, in Table 6. Accordingly, one aspect of the invention involves the treatment of a cancer situated in a tissue listed in Table 7 with an antigenic composition comprising antigenic determinants of the bacterial species that are listed in Table 6, where the regions of endogenous flora linked to the site of the tumor in Table 7 match the regions of endogenous flora linked to the bacterial species in Table 6. The examples provided in Tables 6 and 7 may be used to formulate antigenic compositions for use in treating inflammatory conditions, cancers, for example as an anti-inflammatory treatment for cancers, inflammation associated with cancers, or inflammatory conditions situated in the organs identified in Tables 6 and 7.

TABLE 7 Tissue/Organ Pathogenicity of Endogenous Flora organ site GU Duodenum/ Tissue Skin Respiratory Genital System Mouth Stomach Jejunum Ileum Colon Skin x x Soft tissue x (i.e. fat and muscle) (e.g., sarcoma) Breast x x Lymph x x x nodes: head and neck Lymph x ✓ ✓ nodes: axillae/arm Lymph x ✓ ✓ nodes: mediastinal Lymph x nodes: pulmonary hilum Lymph x ✓ x x x x nodes: intra- abdominal Lymph x X ✓ ✓ nodes: inguinal/ leg Hematological ✓ ✓ ✓ (e.g. leukemias, multiple myeloma) Bone x ✓ ✓ Joints x ✓ ✓ ✓ Meninges x x Brain ✓ ✓ ✓ Spinal cord ✓ ✓ ✓ Eye/Orbit x x X x Salivary x glands Oral x Tonsil x x Nasopharynx/ x x Sinus Thyroid ✓ ✓ ✓ Larynx x x Lung/Trachea/ x Bronchi Pleura ✓ x ✓ ✓ Mediastinum x Heart ✓ ✓ Esophagus x Stomach x Small x x bowel Colon/ x Rectum Anus x x Perineum x x Liver ✓ ✓ ✓ Gallbladder x Biliary tract x Pancreas x Spleen ✓ ✓ ✓ Adrenal ✓ ✓ ✓ gland Kidney ✓ x ✓ ✓ Ureter x Bladder ✓ x x Peritoneum x x x x Retroperitoneal x x x x x area Prostate x x Testicle x x Penis x x x Ovary/ x x x Adnexae Uterus x x x Cervix x x x Vagina x x Vulva x x * Bacteria have access to tissues/organs either through: Contiguous spread (x) or Bacteremic spread: (✓).

In accordance with the combined information in Tables 6 and 7, cancers located in the tissues or organs set out in column 1 of Table 7 may be treated with antigenic compositions comprising antigenic determinants of the corresponding bacterial species of Table 6, so that the column headings in Table 7 are in effect replaced with the bacterial species of Table 6.

In some embodiments, microbial pathogens for use in the invention may be exongenous bacterial pathogens. For example, the organisms listed in Table 8 may be used as microbial pathogens to formulate antigenic compositions, or antigenic compositions having those pathogens may be selected, for use to treat inflammatory conditions, cancers, for example as an anti-inflammatory treatment for cancers, inflammation associated with cancers, or inflammatory conditions situated in the tissues or organs listed with the relevant organism in Table 8. In some embodiments, antigenic determinants of both endogenous and exogenous bacterial species targeted to a specific tissue or organ may be used in combination. For example, an antigenic composition derived from, or specific for, Clostridium difficile, may be used to treat inflammatory conditions, cancers, for example as an anti-inflammatory treatment for cancers, inflammation associated with cancers, or inflammatory conditions situated in the colon.

TABLE 8 Exogenous Bacterial Human Pathogens, and their Sites of Infection bacterial species tissue/organ sites Achromobacter hematological, skin, soft tissue, lung/trachea/bronchi, spp. peritoneum, meninges, bile duct, gallbladder, kidney, bladder, ureter Actinomadura skin, soft tissue, lung/trachea/bronchi, mediastinum, brain, spp. spinal cord, hematological, meninges, joints Aerobacter spp. small bowel, colon, hematological, peritoneum Aerococcus spp. hematological, heart, bone, kidney, bladder, ureter, meninges Alcaligenes spp. lung/trachea/bronchi Anaplasma spp. meninges, hematological, liver, spleen, bone, lung/trachea/bronchi Bacillus anthracis lung/trachea/bronchi, lymph nodes pulmonary hilum, mediastinum, meninges, skin, nasopharynx, tonsil, oral, small bowel, colon, hematological Bacillus cereus colon, eye, hematological other Bacillus hematological, bone, meninges, brain, heart, spp. lung/trachea/bronchi, mediastinum, skin, soft tissue, colon, stomach, small bowel, eye Balneatrix spp. lung/trachea/bronchi, meninges, hematological Bartonella skin, hematological, liver, muscle, lymph nodes, joints bacilliformis Bartonella brain, spinal cord, hematological, skin, liver, bone, pleura, henselae lung/trachea/bronchi, mediastinum, axillary and inguinal lymph nodes, eye, joints Bartonella skin, hematological, liver, spleen, joints quintana Bergeyella skin, soft tissue, meninges, hematological, zoohelcum lung/trachea/bronchi Bordetella lung/trachea/bronchi, hematological holmesii Bordetella nasopharynx, tonsil, lung/trachea/bronchi parapertussis Bordetella nasopharynx, tonsil, lung/trachea/bronchi pertussis Borrelia meninges, brain, spinal cord, skin, eye, hematological, burgdorferi inguinal/axillary/cervical lymph nodes, muscle, liver, spleen, nasopharynx, lung/trachea/bronchi, testes, joints Borrelia brain, spinal cord, hematological, small bowel, liver, recurrentis spleen, salivary glands, lung/trachea/bronchi, lymph nodes, eye, skin Brevundimonas peritoneum, hematological, skin, soft tissue spp. Brucella spp. lung/trachea/bronchi, lymph nodes pulmonary hilum, meninges, brain, spinal cord, lymph nodes, mediastinum, bone, eye, small bowel, colon, liver, biliary tract, kidney, ureter, bladder, hematological, skin, testes, spleen, prostate, joints Burkholderia hematological, meninges, lung/trachea/bronchi gladioli Burkholderia lung/trachea/bronchi, skin, soft tissue, liver, spleen, mallei muscle, lymph nodes pulmonary hilum, mediastinal lymph nodes, mediastinum, head and neck lymph nodes, hematological Burkholderia lung/trachea/bronchi, skin, kidney, bladder, ureter, soft pseudomallei tissue, bone, brain, spinal cord, muscle, hematological, prostate, kidney, ureter, meninges Calymmatobacterium skin, penis, vulva, soft tissue, vagina, cervix, bone, granulomatis hematological, inguinal lymph nodes Campylobacter small bowel, colon coli Campylobacter lung/trachea/bronchi, small bowel, colon, meninges, brain, fetus peritoneum, bone, gallbladder, ovaries, hematological, heart, kidney, bladder, ureter Campylobacter colon, hematological, gallbladder, pancreas, bladder, jejuni bone, meninges Campylobacter small bowel, colon sputorum Capnoctyophaga skin, soft tissue, meninges, hematological, bone, canimorsus lung/trachea/bronchi, eye Capnoctyophaga skin, soft tissue, meninges, hematological, bone, cynodegmi lung/trachea/bronchi, eye CDC groups EF- hematological, eye, skin, soft tissue 4a and EF-4b Chlamydia lung/trachea/bronchi, lymph nodes pulmonary hilum, liver, pneumoniae brain, meninges, skin, thyroid, pancreas, hematological Chlamydia psittaci lung/trachea/bronchi, lymph nodes pulmonary hilum, mediastinum, liver, brain, meninges, hematological, skin, thyroid, pancreas Chlamydia inguinal lymph nodes, penis, vulva, vagina, cervix, uterus, trachomatis ovaries and adnexae, peritoneum, prostate, eye Chlamydophila laryngx, trachea/bronchi, hematological pneumoniae Chromobacterium hematological, liver, spleen, lung/trachea/bronchi, kidney, violaceum bladder, ureter, eye/orbit, bone, brain, meninges, spinal cord Chlamydophila lung/trachea/bronchi psittaci Chryseobacterium meninges, lung/trachea/bronchi, hematological spp. Clostridium small bowel, colon, stomach, skin, soft tissue, bifermentans hematological Clostridium colon, small bowel, skin botulinum Clostridium colon difficile Clostridium indolis small bowel, colon, stomach, skin, soft tissue, hematological Clostridium small bowel, colon, stomach, skin, soft tissue, mangenolii hematological Clostridium small bowel, colon, stomach, skin, soft tissue, perfringens hematological, heart Clostridium small bowel, colon, stomach, skin, soft tissue, sordellii hematological Clostridium small bowel, colon, stomach, skin, soft tissue, sporogenes hematological Clostridium small bowel, colon, stomach, skin, soft tissue, subterminale hematological Clostridium tetani skin, soft tissue Comamonas spp. hematological, peritoneum, eye Corynebacterium neck/axillary/inguinal/mediastinal lymph nodes, lymph pseudotuberculosis nodes pulmonary hilum, lung/trachea/bronchi, mediastinum Coxiella burnetii lung/bronchi/trachea, brain, spinal cord, liver, bone, joints Edwarsiella tarda skin, soft tissue, liver, meninges, small bowel, colon, bone, uterus, ovaries Ehrlichia spp. meninges, brain, spinal cord, hematological, bone, liver, kidney, spleen, lymph nodes Erysipelothrix skin, hematological, bone, brain, peritoneum rhusiopathiae Francisella nasopharynx, oral, tonsil, lung/trachea/bronchi, skin, tularensis axillary/head and neck/inguinal lymph nodes, hematological, eye, small bowel Fusobacterium skin, soft tissue, hematological spp. Gordonia spp. skin, soft tissue, lung/trachea/bronchi, mediastinum, brain, spinal cord, hematological, meninges, eye Haemophilus skin, inguinal lymph nodes, penis, vulva, vagina ducreyi Helicobacter stomach pylori Legionella spp. lung/trachea/bronchi, lymph nodes pulmonary hilum, hematological, brain, spinal cord, muscle, pancreas Leptospirosis spp. lung/trachea/bronchi, pancreas, meninges, brain, spinal cord, skin, lymph nodes, eye, hematological, nasopharynx, oral, tonsil, kidney, liver, spleen Listeria hematological, brain, meninges, spinal cord, small bowel, monocytogenes colon Methylobacterium hematological, peritoneum, skin, soft tissue, bone spp. Mycobacterium lung/bronchi/trachea, lymph nodes pulmonary hilum, avium prostate, pancreas, spleen, skin, neck lymph nodes, esophagus, bone, hematological Mycobacterium colon, small bowel, joints bovis Mycobacterium lung/bronchi/trachea, lymph nodes pulmonary hilum, kansasii prostate, bone Mycobacterium skin, soft tissues, testes, eye leprae Mycobacterium skin, soft tissue, bone marinum Mycobacterium head and neck lymph nodes scrofulaceum Mycobacterium lung/bronchi/trachea, lymph nodes pulmonary hilum, tuberculosis prostate, peritoneum, pancreas, spleen, lymph nodes, small bowel, meninges, brain, spinal cord, kidney, ureter, bladder, muscle, esophagus, colon, testes, eye, ovaries, cervix, vagina, uterus, mediastinum, larynx, skin, hematological, pleura, joints Mycobacterium skin, soft tissue ulcerans other lung/bronchi/trachea, lymph nodes pulmonary hilum, skin, Mycobacterium soft tissues, bone, head and neck lymph nodes, joints spp. Myroides spp. kidney, bladder, ureter, skin, soft tissue, hematological Neisseria nasopharyx, oral, tonsil, prostate, penis, vagina, cervix, gonorrhoeae uterus, ovary/adnexae, peritoneum, skin, muscle, bone, liver, hematological, head and neck and inguinal and intra- abdominal lymph nodes, anus, joints Neorickettsia hematological, bone, lymph nodes, liver, spleen sennetsu Nocardia spp. lung/bronchi/trachea, pancreas, meninges, spinal cord, brain, skin, soft tissue, eye, bone, kidney, heart, hematological Orientia meninges, brain, spinal cord, hematological, skin, inguinal tsutsugamushi and axillary lymph nodes, spleen, lung/bronchi/trachea Pandoraea spp. lung/trachea/bronchi, hematological Pasteurella canis skin, soft tissue, hematological Pasteurella skin, soft tissue, hematological dagmatis Pasteurella skin, soft tissue, hematological stomatis Pediococcus spp. hematological, liver, colon Pityrosporum skin ovale Plesiomonas small bowel, colon, hematological, meninges, bone, gall shigelloides bladder, skin, soft tissue Pseudomonas lung/trachea/bronchi, hemaotogical, skin, soft tissue, bone, aeruginosa meninges, brain, eye, kidney, bladder, ureter, heart, joints other skin, soft tissue, lung/trachea/bronchi, mediastinum, Pseudomonas hematological spp. Ralstonia spp. hematological, meninges, bone Rhizobium spp. hematological, peritoneum, eye, kidney, bladder, ureter Rhodococcus lung/trachea/bronchi, hematological, brain, skin, lymph spp. nodes, bone, mediastinum, liver, spleen, soft tissue, spinal cord, meninges Rickettsia akari skin Rickettsia conorii lung/bronchi/trachea, lymph nodes pulmonary hilum, meninges, brain, spinal cord, hematolofical, skin, kidney, liver, spleen, pancreas Rickettsia felis skin, brain, spinal cord Rickettsia meninges, brain, spinal cord, hematological, prowazekii lung/bronchi/trachea, skin, spleen Rickettsia lung/bronchi/trachea, lymph nodes pulmonary hilum, rickettsiae meninges, brain, spinal cord, hematological, muscle, small bowel, liver, skin Rickettsia slovaca skin, head and neck lymph nodes Rickettsia typhi meninges, hematological, liver, kidney, brain, lung/bronchi/trachea, spleen Roseomonas spp. hematological, peritoneum, skin, soft tissue, bladder, kidney, ureter Salmonella spp. lung/bronchi/trachea, pancreas, spleen, intra-abdominal lymph nodes, stomach, small bowel, colon, meninges, skin, muscle, bone, hematological, heart, joints Shewanella spp. skin, soft tissue, eye, bone, hematological, peritoneum Shigella boydii colon Shigella colon dysenteriae Shigella flexneri colon Shigella sonnei colon Sphingobacterium brain, meninges, spinal cord, eye, skin, soft tissue spp. Sphingomonas hematological, meninges, peritoneum, skin, soft tissue, spp. kidney, bladder, ureter Spirillum minus skin, axillary/inguinal/neck lymph nodes, hematological, liver, spleen other Spirillum colon spp. Stenotrophomonas meninges, hematological, peritoneum, maltophilia lung/trachea/bronchi, eye, kidney, bladder, ureter, skin, soft tissue Streptobacillus skin, bone, hematological, lung/trachea/bronchi, meninges, moniliformis brain, liver, spleen Streptococcus skin, hematological, soft tissue iniae Streptococcus small bowel, nasopharynx, bone, meninges, zooepidemicus hematological, head and neck lymph nodes Streptomices spp. skin, soft tissue, lung/trachea/bronchi, mediastinum, brain, spinal cord, hematological, meninges, joints Treponema nasopharynx, tonsil, oral, meninges, brain, spinal cord, pallidum penis, vulva, vagina, anus, cervix, eye, hematological, inguinal and head and neck lymph nodes Tropheryma brain, spinal cord, hematological, small bowel, colon, whipplei heart, lung/trachea/bronchi, eye Tsukamurella skin, soft tissue, lung/trachea/bronchi, mediastinum, brain, spp. spinal cord, hematological, meninges Vibrio cholerae colon, small bowel Vibrio hematological, meninges cincinnatiensis Vibrio damsela skin, soft tissue Vibrio fluvialis small bowel, colon Vibrio furnissii small bowel, colon Vibrio hollisae small bowel, colon, skin, soft tissue Vibrio hematological metschnikovii Vibrio colon, small bowel parahaemolyticus Vibrio vulnificus soft tissue, blood, skin Yersinia nasopharynx, tonsil, small bowel, intra-abdominal lymph enterocolitica nodes, colon, muscle, lung/trachea/bronchi, liver, spleen, hematological, joints Yersinia pestis lung/trachea/bronchi, lymph nodes pulmonary hilum, inguinal/axillary/neck lymph nodes, oral, tonsil, hematological, skin, joints Yersinia small bowel, colon, abdominal lymph nodes, joints pseudotuberculosis

In some embodiments, microbial pathogens for use in the invention may be viral pathogens. Table 9 provides an exemplary list of viral pathogens together with the tissue and organ sites for which each viral species is reportedly a pathogen. Accordingly, one aspect of the invention involves utilizing immunogenic compositions that are specific for the named viruses to treat an inflammatory condition, a cancer, for example as an anti-inflammatory treatment for cancers, or inflammation associated with cancers or other inflammatory condition, situated in the organs or tissues that are identified adjacent to the name of the virus in Table 9. For example, an antigenic composition derived from, or specific for, a vaccinia virus, may be used to treat an inflammatory condition, a cancer, for example as an anti-inflammatory treatment for cancers, or inflammation associated with cancers or other inflammatory condition, situated in the skin, hematological tissues, lymph nodes, brain, spinal cord, eye or heart.

TABLE 9 Viral Human Pathogens and Their Sites of Infection virus tissue/organ sites Vaccinia skin, hematological, lymph nodes, brain, spinal cord, eye, heart Variola (smallpox) skin, hematological, lymph nodes, brain Monkeypox skin, hematological, head and neck lymph nodes, brain, eye, lung/trachea/bronchi, pulmonary hilar lymph nodes, mediastinum, nasopharynx Cowpox skin, hematological, lymph nodes Parapoxviruses Skin Molluscum skin contagiosum Tanapox skin, hematological, axillary and inguinal lymph nodes Herpes Simplex nasopharynx, oral, tonsil, hematological, virus (1 and 2) lung/bronchi/trachea, pancreas, meninges, brain, spinal cord, inguinal and head/neck lymph nodes, penis, vulva, perineum, esophagus, liver, eye, skin, rectum, tonsil, mediastinum, anus, vagina, cervix Varicella-zoster nasopharynx, sinus, lung/trachea/bronchi, pulmonary hilar lymph nodes, hematological, pancreas, meninges, brain, spinal cord, esophagus, liver, eye, skin, heart, mediastinum Cytomegalovirus nasopharynx, lymph nodes, tonsil, hematological, lung/trachea/bronchi, pancreas, abdominal lymph nodes, brain, spinal cord, esophagus, small bowel, colon/rectum, eye, liver, heart, skin, mediastinum, esophagus Epstein-Barr virus nasopharynx, tonsil, oral, lymph nodes, hematological, lung, abdominal lymph nodes, brain, spinal cord, muscles, esophagus, liver, heart, skin, spleen, kidney, muscle, heart, lung/trachea/bronchi, pulmonary hilar lymph nodes, mediastinum Human herpesvirus 6 skin, hematological, lung/trachea/bronchi, pulmonary hilar lymph nodes, brain, meninges, liver Human herpesvirus 7 skin, brain, liver Human herpesvirus 8 nasopharynx, tonsil, hematological, skin, spleen, head and neck lymph nodes Simian herpes B brain, spinal cord, skin, hematological, lymph nodes virus Adenovirus nasopharynx, oral, larynx, trachea, bronchi, lung, lymph nodes, meninges, brain, spinal cord, small bowel, colon, liver, intra-abdominal lymph nodes, mediastinum, bladder, sinus, hematological, ureter, kidney, bladder, thyroid, heart BK virus kidney Human skin, anus, penis, vulva, cervix, vagina, oral papillomavirus Hepatitis B virus liver, pancreas, hematological, bone, joints Hepatitis D virus liver Parvovirus B19 skin, hematological, nasopharynx, bone, kidney, heart, liver, brain, meninges, joints Orthoreoviruses nasopharynx, small bowel, colon, oral, sinus, lymph nodes, skin, lung/trachea/bronchi, meninges, brain, spinal cord, liver Orbiviruses brain, muscle, hematological, Coltiviruses hematological, skin, muscle, oral, spleen, lymph nodes, meninges, brain Rotaviruses small bowel, colon, liver, hematological, pancreas, nasopharynx, billiary tract, meninges, brain Alphaviruses brain, spinal cord, small bowel, colon, hematological, skin, bone Rubella skin, hematological, head and neck lymph nodes, spleen, nasopharynx, bone, brain, tonsil, bronchi, liver, heart, joints Yellow fever virus hematological, liver, lung/trachea/bronchi, kidney, adrenal gland, spleen, lymph nodes, stomach, kidney Dengue fever virus hematological, lymph nodes, skin, spleen, muscle, liver, brain, nasopharynx, joints Japanese brain, hematological, spinal cord encephalitis virus West Nile brain, hematological, spinal cord, muscle, lymph nodes, encephalitis virus liver, spleen, pancreas, meninges St. Louis brain, hematological, spinal cord, meninges, muscle, encephalitis virus nasopharynx Tick-borne brain, hematological, spinal cord, muscle, meninges encephalitis virus other Flaviviruses hematological, brain, meninges, bone, muscles, skin, lymph nodes Hepatitis C virus hematological, liver, joints Hepatitis G virus liver Coronaviruses nasopharynx, sinus, oral, tonsil, larynx, lung/trachea/bronchi, pulmonary hilar lymph nodes, small bowel, colon, tonsil, hematological Toroviruses small bowel, colon, hematological Parainfluenza nasopharynx, sinus, tonsil, oral, larynx, viruses lung/trachea/bronchi, pulmonary hilar lymph nodes, meninges, hematological, mediastinum Mumps virus salivary glands, pancreas, brain, spinal cord, liver, testes, hematological, meninges, ovaries, bone, heart, kidney, thyroid, prostate, breast, joints Respiratory syncytial nasopharynx, tonsil, sinus, lung/trachea/bronchi, virus pulmonary hilar lymph nodes, mediastinum, hematological, oral, pleura Human nasopharynx, lung/trachea/bronchi, pulmonary hilar metapneumovirus lymph nodes, tonsil, sinus, mediastinum, hematological, oral, pleura, larynx, eye, skin, small bowel, colon Rubeola nasopharynx, sinus, hematological, lung/trachea/bronchi, pulmonary hilar lymph nodes, intra-abdominal lymph nodes, meninges, brain, spinal cord, liver, spleen, lymph nodes, skin, thymus, eye, oral, heart Hendra virus brain, meninges, lung/trachea/bronchi, kidney, hematological, muscle, Nipah virus brain, meninges, spleen, lymph nodes, thymus, lung/trachea/bronchi, kidneys, brain, spinal cord, meninges, hematological Vesicular stomatitis hematological, muscle, oral, tonsil, nasopharyngeal, virus lymph nodes, small bowel, colon Rabies virus skin, meninges, brain, spinal cord, oral, nasopharynx, salivary glands, hematological Lyssaviruses brain, spinal cord Influenza virus nasopharynx, laryngx, lung/trachea/bronchi, pulmonary hilar lymph nodes, meninges, muscle, hematological, mediastinum, muscle, sinus, tonsil, oral, eye, pleura, brain, spinal cord, salivary glands, thyroid, heart California hematological, brain, meninges encephalitis virus Hantaviruses hematological, kidney, eye, skin, oral, muscle, lung/trachea/bronchi other Bunyaviruses brain, hematological, muscle, meninges, spinal cord Lymphocytic hematological, muscle, lymph nodes, skin, brain, choriomeningitis meninges, testes, bone virus Lassa virus nasopharynx, brain, spinal cord, lung/trachea/bronchi, pulmonary hilar lymph nodes, mediastinum, muscle, testes, eye, heart, Machupo virus brain, meninges, hematological, muscle, eye, skin, lymph nodes, nasopharynx, small bowel, colon Junin virus brain, meninges, hematological, muscle, eye, skin, lymph nodes, nasopharynx, small bowel, colon Human T-Cell hematological, skin, lymph nodes, muscle, eye, bone, Lymphotropic lung, pulmonary hilar lymph nodes, spinal cord, brain viruses Poliovirus nasopharynx, lung/trachea/bronchi, pulmonary hilar lymph nodes, small bowel, neck and intra-abdominal lymph nodes, colon, hematological, liver, spleen, skin, brain, spinal cord, meninges, heart Coxsackieviruses nasopharynx, larynx, oral, tonsil, lung/trachea/bronchi, pulmonary hilar lymph nodes, mediastinum, pancreas, muscle, brain, meninges, small bowel, neck and intra- abdominal lymph nodes, colon, hematological, spleen, skin, eye, sinus, liver, testes, bone, pleura, salivary glands, heart Echoviruses nasopharynx, oral, tonsil, lung/trachea/bronchi, pulmonary hilar lymph nodes, muscle, brain, meninges, small bowel, neck and intra-abdominal lymph nodes, colon, hematological, mediastinum, spleen, skin, eye, sinus, liver, pancreas, testes, bone, salivary glands, heart other Enteroviruses lung/trachea/bronchi, pulmonary hilar lymph nodes, meninges, brain, skin, heart, joints Hepatitis A virus small bowel, colon, hematological, liver, spleen, brain, spinal cord, gallbladder, pancreas, kidney Rhinoviruses nasopharynx, sinus, oral, tonsil, larynx, lung/trachea/bronchi, pulmonary hilar lymph nodes Noroviruses and small bowel, colon other Caliciviruses Astroviruses small bowel, colon Picobirnaviruses small bowel, colon Hepatitis E virus liver, small bowel, colon, hematological

The cumulative information in Tables 6 through 9 provides an extensive identification of microbial pathogens that may be used in the formulation of antigenic compositions of the invention, together with an identification of the tissues or organs in which these organisms are pathogenic, and accordingly identifies the correspondence between selected tissues or organs in which an inflammatory condition, cancer, or disease characterized by inflammation is situated, and the organisms that may be used to produce antigenic formulations for treating the condition.

In some embodiments, the microbial pathogen selected for use in antigenic compositions of the invention may be one that is a common cause of acute infection in the tissue or organ in which the cancer to be treated is situated. Table 10 identifies bacterial and viral pathogens of this kind, together with the tissues and organs in which they commonly cause infection. Accordingly, in selected embodiments, a cancer residing in a tissue identified in the first column of Table 10 may be treated with an antigenic composition that comprises antigenic determinants for one or more of the pathogenic organisms listed in the second column of Table 10. For example, a cancer residing in the skin may be treated with an antigenic composition comprising antigenic determinants of one or more of the following organisms: Staphylococcus aureus, Beta hemolytic streptococci group A, B, C and G, Corynebacterium diptheriae, Corynebacterium ulcerans, Pseudomonas aeruginosa, rubeola, rubella, varicella-zoster, echoviruses, coxsackieviruses, adenovirus, vaccinia, herpes simplex, or parvo B19.

TABLE 10 Common Causes of Acute Infection (Bacterial and Viruses) For Each Tissue/Organ Site Tissue/organ Common Bacterial or Viral Pathogens of specific site tissue/organ site Skin Staphylococcus aureus, Beta hemolytic streptococci group A, B, C and G, Corynebacterium diptheriae, Corynebacterium ulcerans, Pseudomonas aeruginosa rubeola, rubella, varicella-zoster, echoviruses, coxsackieviruses, adenovirus, vaccinia, herpes simplex, parvo B19 Soft tissue (i.e. Streptococcus pyogenes, Staphylococcus aureus, fat and muscle) Clostridium perfringens, other Clostridium spp. (e.g., sarcoma) influenza, coxsackieviruses Breast Staphylococcus aureus, Streptococcus pyogenes Lymph nodes: Staphylococcus aureus, Streptococcus pyogenes head and neck Epstein-Barr, cytomegalovirus, adenovirus, measles, rubella, herpes simplex, coxsackieviruses, varicella-zoster Lymph nodes: Staphylococcus aureus, Streptococcus pyogenes axillae/arm measles, rubella, Epstein-Barr, cytomegalovirus, adenovirus, varicella-zoster Lymph nodes: viridans streptococci, Peptococcus spp., mediastinal Peptostreptococcus spp., Bacteroides spp., Fusobacterium spp., Mycobacterium tuberculosis measles, rubella, Epstein-Barr, cytomegalovirus, varicella- zoster, adenovirus Lymph nodes: Streptococcus pneumoniae, Moraxella catarrhalis, pulmonary Mycoplasma pneumoniae, Klebsiella pneumoniae, hilum Haemophilus influenza, Chlamydophila pneumoniae, Bordetella pertussis, Mycobacterium tuberculosis influenza, adenovirus, rhinovirus, coronavirus, parainfluenza, respiratory syncytial virus, human metapneumovirus, coxsackievirus Lymph nodes: Yersinia enterocolitica, Yersinia pseudotuberculosis, intra-abdominal Salmonella spp., Streptococcus pyogenes, Escherichia coli, Staphylococcus aureus, Mycobacterium tuberculosis measles, rubella, Epstein-Barr, cytomegalovirus, varicella- zoster, adenovirus, influenza, coxsackieviruses Lymph nodes: Staphylococcus aureus, Streptococcus pyogenes inguinal/leg measles, rubella, Epstein-Barr, cytomegalovirus, herpes simplex Hematological Staphylococcus aureus, Streptococcus pyogenes, (e.g. leukemias, coagulase-negative staphylococci, Enterococcus spp., multiple myeloma) Escherichia coli, Klebsiella spp., Enterobacter spp., Proteus spp., Pseudomonas aeruginosa, Bacteroides fragilis, Streptococcus pneumoniae, group B streptococci rubeola, rubella, varicella-zoster, echoviruses, coxsackieviruses, adenovirus, Epstein-Barr, cytomegalovirus, herpes simplex Bone Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus agalactiae, other streptococci spp., Escherichia coli, Pseudomonas spp., Enterobacter spp., Proteus spp., Serratia spp. parvovirus B19, rubella, hepatitis B Joint Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus agalactiae, other streptococci spp., Escherichia coli, Pseudomonas spp., Enterobacter spp., Proteus spp., Serratia spp., Neisseria gonorrhea, salmonella species, Mycobacterim tuberculosis, Hemophilus influenza parvovirus B19, rubella, hepatitis B Scedosporium prolificans Meninges Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus agalactiae, Listeria monocytogenes echoviruses, coxsackieviruses, other enteroviruses, mumps Brain Streptococcus spp. (including S. anginosus, S. constellatus, S. intermedius), Staphylococcus aureus, Bacteroides spp., Prevotella spp., Proteus spp., Escherichia coli, Klebsiella spp., Pseudomonas spp., Enterobacter spp., Borrelia burgdorferi coxsackieviruses, echoviruses, poliovirus, other enteroviruses, mumps, herpes simplex, varicella-zoster, flaviviruses, bunyaviruses Spinal cord Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus agalactiae, Listeria monocytogenes, Borrelia burgdorferi coxsackieviruses, echoviruses, poliovirus, other enteroviruses, mumps, herpes simplex, varicella-zoster, flaviviruses, bunyaviruses Eye/Orbit Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus milleri, Escherichia coli, Bacillus cereus, Chlamydia trachomatis, Haemophilus influenza, Pseudomonas spp., Klebsiella spp., Treponema pallidum adenoviruses, herpes simplex, varicella-zoster, cytomegalovirus Salivary glands Staphylococcus aureus, viridans streptococci (e.g., Streptococcus salivarius, Streptococcus sanguis, Streptococcus mutans), Peptostreptococcus spp., Bacteroides spp., and other oral anaerobes mumps, influenza, enteroviruses, rabies Oral Prevotella melaninogenicus, anaerobic streptococci, viridans streptococci, Actinomyces spp., Peptostreptococcus spp., Bacteroides spp., and other oral anaerobes herpes simplex, coxsackieviruses, Epstein-Barr Tonsil Streptococcus pyogenes, Group C and G B-hemolytic streptococci rhinoviruses, influenza, coronavirus, adenovirus, parainfluenza, respiratory syncytial virus, herpes simplex Sinus Streptococcus pneumoniae, Haemophilus influenza, Moraxella catarrhalis, α-streptococci, anaerobic bacteria (e.g., Prevotella spp.), Staphylococcus aureus rhinoviruses, influenza, adenovirus, parainfluenza Nasopharynx Streptococcus pyogenes, Group C and G B-hemolytic streptococci rhinoviruses, influenza, coronavirus, adenovirus, parainfluenza, respiratory syncytial virus, herpes simplex Thyroid Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae mumps, influenza Larynx Mycoplasma pneumoniae, Chlamydophila pneumoniae, Streptococcus pyogenes rhinovirus, influenza, parainfluenza, adenovirus, corona virus, human metapneumovirus Trachea Mycoplasma pneumoniae parainfluenza, influenza, respiratory syncytial virus, adenovirus Bronchi Mycoplasma pneumoniae, Chlamydophila pneumoniae, Bordetella pertussis, Streptococcus pneumoniae, Haemophilus influenzae influenza, adenovirus, rhinovirus, coronavirus, parainfluenza, respiratory syncytial virus, human metapneumovirus, coxsackievirus Lung Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae, Klebsiella pneumoniae, Haemophilus influenza influenza, adenovirus, respiratory syncytial virus, parainfluenza Pleura Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, Bacteroides fragilis, Prevotella spp., Fusobacterium nucleatum, peptostreptococcus spp., Mycobacterium tuberculosis influenza, adenovirus, respiratory syncytial virus, parainfluenza Mediastinum viridans streptococci, Peptococcus spp., Peptostreptococcus spp., Bacteroides spp., Fusobacterium spp. measles, rubella, Epstein-Barr, cytomegalovirus Heart Streptococcus spp. (including S. mitior, S. bovis, S. sanguis, S. mutans, S. anginosus), Enterococcus spp., Staphylococcus spp., Corynebacterium diptheriae, Clostridium perfringens, Neisseria meningitidis, Salmonella spp. enteroviruses, coxsackieviruses, echoviruses, poliovirus, adenovirus, mumps, rubeola, influenza Esophagus Actinomyces spp., Mycobacterium avium, Mycobacterium tuberculosis, Streptococcus spp. cytomegalovirus, herpes simplex, varicella-zoster Stomach Streptococcus pyogenes, Helicobacter pylori cytomegalovirus, herpes simplex, Epstein-Barr, rotaviruses, noroviruses, adenoviruses Small bowel Escherichia coli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, Shigella flexneri adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, cytomegalovirus Colon/Rectum Escherichia coli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonella enteriditis, Yersinia enterocolitica, Shigella flexneri adenoviruses, astroviruses, caliciviruses, noroviruses, rotaviruses, cytomegalovirus Anus Streptococcus pyogenes, Bacteroides spp., Fusobacterium spp., anaerobic streptococci, Clostridium spp., E. coli, Enterobacter spp., Pseudomonas aeruginosa, Treponema pallidum herpes simplex Perineum Escherichia coli, Klebsiella spp., Enterococcus spp., Bacteroides spp., Fusobacterium spp., Clostridium spp., Pseudomonas aeruginosa, anaerobic streptococci, Clostridium spp., E. coli, Enterobacter spp. herpes simplex Liver Escherichia coli, Klebsiella spp., Streptococcus (anginosus group), Enterococcus spp., other viridans streptococci, Bacteroides spp. hepatitis A, Epstein-Barr, herpes simplex, mumps, rubella, rubeola, varicella-zoster, coxsackieviruses, adenovirus Gallbladder Escherichia coli, Klebsiella spp., Enterobacter spp., enterococci, Bacteroides spp., Fusobacterium spp., Clostridium spp., Salmonella enteriditis, Yersinia enterocolitica, Shigella flexneri Biliary tract Escherichia coli, Klebsiella spp., Enterobacter spp., Enterococci spp., Bacteroides spp., Fusobacterium spp., Clostridium spp., Salmonella enteriditis, Yersinia enterocolitica, Shigella flexneri hepatitis A, Epstein-Barr, herpes simplex, mumps, rubella, rubeola, varicella-zoster, cocsackieviruses, adenovirus Pancreas Escherichia coli, Klebsiella spp., Enterococcus spp., Pseudomonas spp., Staphylococcal spp., Mycoplasma spp., Salmonella typhi, Leptospirosis spp., Legionella spp. mumps, coxsackievirus, hepatitis B, cytomegalovirus, herpes simplex 2, varicella-zoster Spleen Streptococcus spp., Staphylococcus spp., Salmonella spp., Pseudomonas spp., Escherichia coli, Enterococcus spp. Epstein-Barr, cytomegalovirus, adenovirus, measles, rubella, coxsackieviruses, varicella-zoster Adrenal gland Streptococcus spp., Staphylococcus spp., Salmonella spp., Pseudomonas spp., Escherichia coli, Enterococcus spp. varicella-zoster Kidney Escherichia coli, Proteus mirabilis, Proteus vulgatus, Providentia spp., Morganella spp., Enterococcus faecalis, Pseudomonas aeruginosa BK virus, mumps Ureter Escherichia coli, Proteus mirabilis, Proteus vulgatus, Providentia spp., Morganella spp., Enterococcus spp. Bladder Escherichia coli, Proteus mirabilis, Proteus vulgatus, Providentia spp., Morganella spp., Enterococcus faecalis, Corynebacterium jekeum adenovirus, cytomegalovirus Peritoneum Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumonia, Escherichia coli, Klebsiella spp., Proteus spp., Enterococci spp., Bacteroides fragilis, Prevotella melaninogenica, Peptococcus spp., Peptostreptococcus spp., Fusobacterium spp., Clostridium spp. Retroperitoneal Escherichia coli, Staphylococcus aureus area Prostate Escherichia coli, Klebsiella spp., Enterobacter spp., Proteus mirabilis, Enterococci spp., Pseudomonas spp., Corynebacterium spp., Neisseria gonorrhoeae herpes simplex Testicle Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus spp., Streptococcus spp., Salmonella enteriditis mumps, coxsackievirus, lymphocytic choriomeningitis virus Penis Staphylococcus aureus, Streptococcus pyogenes, Neisseria gonorrhoeae, Treponema pallidum herpes simplex, human papillomavirus Ovary/Adnexae Neisseria gonorrhoeae, Chlamydia trachomatis, Gardenerella vaginalis, Prevotella spp., Bacteroides spp., Peptococcus spp. Streptococcus spp., Escherichia coli Uterus Neisseria gonorrhoeae, Chlamydia trachomatis, Gardenerella vaginalis, Prevotella spp., Bacteroides spp., Peptococcus spp., Streptococcus spp., Escherichia coli Cervix Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum herpes simplex Vagina Gardenerella vaginalis, Prevotella spp., Bacteroides spp., peptococci spp., Escherichia coli, Neisseria gonorrhoeae, Chlamydia Trachomatis, Treponema pallidum, herpes simplex Vulva Staphylococcus aureus, Streptococcus pyogenes, Treponema pallidum herpes simplex

In selected embodiments, particular microbial pathogens are suited for treatment of particular inflammatory conditions, including cancers, for example as an anti-inflammatory treatment for cancers, or inflammation associated with cancers or other inflammatory condition, located in the tissue or organ within which the organism is pathogenic, examples of selected embodiments are set out in Table 10. These are exemplary embodiments, and not an exhaustive list of the alternative formulations for use in accordance with the invention.

The specific microbes which commonly cause infection in a specific tissue or organ may vary by geographical location. For example, Mycobacterium tuberculosis is a more common cause of lung infection in some geographical locations and populations than in others and therefore, while M. tuberculosis may not be a common lung pathogen in some geographic and population groups it may be a common lung pathogen in others. Table 10 is thus not an exhaustive list of common pathogens for all geographic locations and population groups. It is understood that a clinical microbiologist skilled in the art could determine the common pathogenic species in a particular geographic area or population group for a specific tissue or organ site in accordance with the invention. For veterinary use, there will of course be specific pathogens that are common in selected tissues of selected species, and this may also vary geographically.

In selected embodiments, the invention involves diagnostic steps to assess a patient's previous exposure to microbial pathogens. For example, the diagnostic steps may include taking a medical history of exposure to selected pathogens, and/or evaluating a patient's immune response to a selected pathogen. For example, a serology test may be conducted to detect antibodies to selected pathogens in a patient's sera. In connection with this aspect of the invention, antigenic determinants of a selected microbial pathogen may be chosen for use in an immunogenic composition on a selected patient based on a diagnostic indication that the patient has had one or more prior exposure(s) to the pathogen, for example by virtue of the presence of antibodies to antigenic determinants of that pathogen in the patient's sera.

In further selected embodiments, the invention involves diagnostic steps to assess a patient's immunological response to treatment with a selected immunogenic composition. For example, the diagnostic steps may include evaluating a patient's immune response to the antigenic determinants of that immunogenic composition, for example using a serological test to detect antibodies to those antigenic determinants. In connection with this aspect of the invention a treatment with a selected immunogenic composition may be continued if the evaluation indicates that there is an active immunological response to the antigenic determinants of that composition, and the vaccine treatment may be discontinued, and an alternative treatment with a different immunogenic composition may be initiated, if the evaluation indicates that there is not a sufficiently active immunological response to the antigenic determinants of the immunogenic composition.

As discussed in the context of Patient R, in selected embodiments, the microbial pathogen selected for use in antigenic compositions of the invention may be one that is the most common cause of acute infection in the tissue or organ in which the cancer to be treated is situated, which may provide particular benefit as illustrated by the case of Patient R. For example, for the treatment of bone cancer, Staphylococcus aureus would be the bacterial species selected; for the treatment of cancer in lung tissue, Streptococcus pneumoniae would be selected; for the treatment of breast cancer, Staphylococcus aureus would be selected; for the treatment of kidney or bladder cancer, Escherichia coli would be selected; and for the treatment of colon cancer, Escherichia coli would be the bacterial species selected. It is understood that a clinical microbiologist skilled in the art could determine the most frequently pathogenic species, bacterial or viral, for each specific tissue or organ in accordance with the invention. In selected embodiments, only antigenic determinants of the most common pathogen for the particular tissue or organ could be used to treat cancers of that tissue or organ. In alternative embodiments, antigenic determinants of the most common pathogen for the particular tissue or organ could be used in combination with antigenic determinants of other pathogens that are known to be pathogenic in the of that particular tissue or organ, preferentially selecting from the more common pathogens.

In some embodiments, the invention provides antigenic compositions in which a threshold proportion of antigenic determinants selected in accordance with the invention are used, relative to any other antigenic determinants in the composition. For example, antigenic compositions may have greater than X % of the antigenic determinants therein derived from pathogenic (or commonly pathogenic, or most commonly pathogenic) species, where X may for example be 10, 30, 40, 50, 60, 70, 80, 90, 95 or 100 (or any integer value between 10 and 100). For example, at least X % of the antigenic determinants in the antigenic composition may be specific for microbial pathogens that are pathogenic (or commonly pathogenic or most commonly pathogenic) in the specific organ or tissue of the patient within which the cancer is situated. Using an alternative measure, of the total number of microbial pathogens in the antigenic composition, at least X % may be selected to be microbial pathogens that are pathogenic (or commonly pathogenic or most commonly pathogenic) in the specific organ or tissue of the patient within which the cancer is situated. In some embodiments, the antigenic composition may accordingly consist essentially of antigenic determinants of one or more microbial pathogens that are each pathogenic (or commonly pathogenic or most commonly pathogenic) in the specific organ or tissue of the patient within which the cancer is situated. The following data illustrates the surprising effectiveness of these selected formulations:

-   (1) The use of MRV (which contains many common respiratory tract     pathogens and Staphylococcus aureus, the most common pathogen of     both breast and bone) was found to be helpful for the treatment of     breast cancer with metastases to the bone (see FIG. 6). However,     survival benefit (survival of patients who were treated with MRV     compared to those who were not) was modest (i.e., median survival of     31 months for patients treated with the vaccine compared to 26     months for patients not treated with the vaccine). On the other     hand, the one patient (Patient R) who was treated with a vaccine     specifically targeted for breast cancer and bone cancer (i.e.,     containing only Staphylococcus aureus, by far the most common cause     of both breast and bone infection) had a remarkable survival     benefit, surviving for more than 17 years. The inclusion, in MRV, of     other bacterial species that do not (or far less commonly) cause     bone infection and commonly cause infection elsewhere (i.e.,     respiratory tract) appears to substantially reduce the benefit of     this vaccine for the treatment of cancer of the breast and bone. -   (2) The survival of stage 3B lung cancer patients treated with     Respivax™ (i.e., median survival of 38 months and 40% 5-year     survival) was substantially greater than the survival of stage 3B     lung cancer patients treated with MRV (i.e., median survival of 18     months and 14% 5-year survival). Respivax™ contains substantially     greater relative concentrations of the bacterial species that     commonly cause lung infection than MRV does. 67% of the bacterial     cell count of Respivax™ is comprised of bacterial species that are     the common causes of lung infection, whereas only 30% of the     bacterial cell count of MRV is comprised of bacterial species that     are the common causes of lung infection. Thus, the composition     having the greater proportion of bacteria that most commonly cause     lung infections, Respivax™, is shown to be more effective for the     treatment of lung cancer than the MRV formulation. -   (3) The survival of stage 4 colon cancer patients treated with MRV     (which does not contain any colon pathogens) was poorer than     patients not treated with a vaccine. This indicates that treatments     that use antigenic determinants that are not derived from microbes     that are pathogenic in the organ or tissue in which the cancer is     situated may not only be ineffective, but may also be deleterious. -   (4) The Murine Studies set out below, and in particular the cancer     cell model data involving treatment with Klebsiella pneumoniae     antigenic determinants alone, compared to treatment with Klebsiella     pneumoniae antigens in conjunction with additional antigens.     The data herein accordingly provide evidence of an increasing     gradation of benefit from pathogenic, to commonly pathogenic, to     most commonly pathogenic for the treatment cancer within a specific     organ or tissue using targeting antigenic compositions that are     derived from microbial pathogens that are pathogenic to that     specific organ or tissue.

In some embodiments, the invention comprises the use of bacterial or viral vaccines that are approved for other purposes (e.g., poliomyelitis vaccine, H. influenza vaccine, meningococcal vaccine, pneumococcal vaccine, influenza vaccine, hepatitis B vaccine, hepatitis A vaccine, diphtheria vaccine, tetanus vaccine, pertussis vaccine, measles vaccine, mumps vaccine, rubella vaccine, varicella vaccine, BCG vaccine, cholera vaccine, Japanese encephalitis vaccine, rabies vaccine, typhoid vaccine, yellow fever vaccine, small pox vaccine, etc.) for use as cancer treatments by selecting a vaccine containing a pathogen (or antigenic constituent of a pathogen) that is pathogenic in the specific organ or tissue of the patient within which the cancer is situated by consulting Tables 6-10. For example, a S. pneumoniae vaccine, either a whole cell vaccine or a vaccine comprised of one or more antigenic components of S. pneumoniae (e.g., pneumococcal polysaccharide-23-valent) could be used to treat cancer at any of the following sites in which S. pneumoniae is listed as a common pathogen in Table 10: pulmonary hilar lymph nodes, hematological cancers, bone, meninges, spinal cord, eye/orbit, sinus, thyroid, bronchi, lungs, pleura or peritoneum. As a further example, a hepatitis B vaccine could be used to treat cancer at any of the following sites in which hepatitis B virus is listed as a pathogen in Table 9, as follows: liver, pancreas, or hematological cancers.

In some embodiments, selected compositions and methods are specifically excluded from the scope of the invention. For example, the use of the following microbial pathogens in the treatment of the following cancers is excluded from some embodiments, so that the claimed invention may extend to particular embodiments with the exception of one or more of the following:

-   a) BCG (Mycobacterium bovis) for the treatment of stomach cancer and     colon cancer, for example by injection; -   b) Mycobacterium w for the treatment of lung cancer, for example by     injection; -   c) Mycobacterium vaccae for the treatment of non-small-cell lung     cancer, for example by injection; -   d) Corynebacterium parvum for the treatment of melanoma, for example     by injection; -   e) Streptococcus pyogenes for the treatment of stomach cancer, for     example by injection; -   f) Nocardia rubra for the treatment of lung cancer or acute     myelogenous leukemia, for example by injection; -   g) Lactobacillus casei for the treatment of cervical cancer, for     example by injection; -   h) Pseudomonas aeruginosa for the treatment of lymphoma and lung     cancer, for example by injection; -   i) Vaccinia for the treatment of melanoma, for example by injection; -   j) Rabies virus for the treatment of melanoma, for example by     injection; -   k) A composition consisting of the combined antigens of the     following bacterial species for the veterinary (or, alternatively,     human) treatment, for example by oral administration, for primary     (or, alternatively, metastatic) cancers situated in the lung:     Streptococcus pneumoniae; Neisseria catarrhalis; Streptococcus     pyogenes; Haemophilus influenzae; Staphylococcus aureus; Klebsiella     pneumoniae. -   l) A composition consisting of the combined antigens of the     following bacterial species for the veterinary (or, alternatively,     human) treatment, for example by oral administration, for primary     (or, alternatively, metastatic) cancers situated in the lung:     Streptococcus pneumoniae; Neisseria catarrhalis; Streptococcus     pyogenes; Haemophilus influenzae; Staphylococcus aureus; Klebsiella     pneumoniae; Klebsiella ozaenae; Streptococcus viridans.

Example 4 Murine Studies

In the following murine studies, the following common materials were utilized: PBS (Gibco), and mice were 7 week-old female C57BL/6.

Example 4A Cancer of the Lung

This section relates to a Lewis lung carcinoma mouse model. The bacterial vaccines used in this experiment were as follows: Streptococcus pneumoniae [cells and broth] vaccine (lot #J049-1 [2×10⁹ ]; Klebsiella pneumoniae [cells and broth] vaccine (lot #J046-1 [2×10⁹ ]; Staphylococcus aureus [cells and broth] vaccine (lot #J041-2 [10×10⁹ ]; Escherichia coli (colon isolate) [cells and broth] vaccine (lot #J047-1 [6×10⁹ ]; Salmonella enterica [cells and broth] vaccine (lot #J31 [15×10⁹ ]; Klebsiella pneumoniae [cells only] vaccine (lot #J048-1 [2×10⁹]; and media only (Klebsiella pneumoniae media) (lot #J046-1). Mice were treated in accordance with the experimental groupings defined in Table 11.

TABLE 11 Experimental Groupings for Lung Cancer Mouse Model Lewis Lung i.v. s.c. injection dose schedule 10e5 cells/100 μl Vial Day: −10, −8, −6, −4, −2, +2, +4, Group Mice Day 0 # Vaccine +6, +8, +10, +12, +14, +16, etc. 1AB   2AB 8   8

1   2 S. pneumoniae [cells and broth] K. pneumoniae [cells and broth] 200x10e6 CFUs/150 μl/mouse 150x10e6 CFUs/75 μl/mouse 3AB 8 3 S. aureus [cells and 1x10e9 broth] CFUs/100 μl/mouse 4AB 8 4 E. coli (colon) [cells 0.9x10e9 and broth] CFUs/150 μl/mouse 5AB 8 5 S. enterica [cells and 1.5x10e9 broth] CFUs/100 μl/mouse 6AB 8 1+ S.+ K. pneumoniae S. 200x10e6 2 [cells and broth]* CFUs/75 μl/mouse K. 150x10e6 CFUs/75 μl/mouse 7AB 8 8 K. pneumoniae [cells 150x10e6 only] CFUs/75 μl/mouse 8ABC 12 9 Media only (K. 75 μl/mouse pneumoniae media) (control) 9AB 8 PBS only none none

Specifically, groups of mice were pre-treated sub-cutaneously with bacterial vaccines on days −10, −8, −6, −4, and −2. On day 0, mice were challenged intravenously with a dosage of 10e5 Lewis lung carcinoma cells (Cedarlane lot#508714). Thereafter, the mice were treated sub-cutaneously with vaccine injections every second day for the duration of the experiment as defined in Table 11. A control group was treated with media only. Animal weights were measured and recorded every 4 days. When mice started showing morbidity the experiment was terminated. Thereafter, all mice were humanely sacrificed and the lungs were surgically removed and weighed. Lungs were placed into the vials with Buoin's fluid and the numbers of lung nodules in each group were counted. These results are illustrated in Table 12. Representative examples of these lungs are depicted in FIG. 14.

TABLE 12 Number of visible lung tumours in mice in each group Number of Group Vaccine visible lung tumours Average Median 1 S. pneumoniae 13, 1, 7, 1, 20, 38, 50, 35 20.6 16.5 2 K. pneumoniae 1, 10, 0, 0, 1, 2, 50 9.1 1 3 S. aureus 1, 5, 3, 15, 10, 57, 43, 38 21.5 12.5 4 E. coli 4, 3, 0, 9, 16, 3, 42, 40 14.6 6.5 5 S. enterica 0, 0, 2, 5, 2, 57, 52 16.8 2 6 S + K. 1, 6, 0, 0, 8, 5, 47, 48 14.3 5.5 pneumoniae 7 K. pneumoniae 0, 3, 0, 0, 0, 1, 46, 49 12.3 0.5 (cells only) 8 Control (medium) 2, 3, 12, 25, 39, 26, 62, 31.7 26 39, 78

The weights of the lungs of mice injected with tumour cells were then compared to the weights of the lungs of mice injected with PBS only, to determine the tumour burden and thus, the therapeutic effect of vaccine treatment. These results are illustrated in Table 13.

TABLE 13 Average lung weight (mg) and tumour weight inhibition (compared to control) in mice immunized with killed bacterial vaccines in intravenously implanted Lewis lung carcinoma model Av. Difference Tumour Lung from Weight weight healthy Inhibition Group Vaccine (mg) mice (%) 1 S. pneumonia (cells and 495 318 30 broth) 2 K. pneumonia (cells and 298 121 73 broth) 3 S. aureus (cells and broth) 485 308 32 4 E. coli (cells and broth) 372 195 57 5 S. enterica (cells and broth) 331 154 66 6 S + K. pneumonia (cells and 374 197 57 broth) 7 K. pneumoniae (cells only) 294 117 74 8 Control (media only) 633 456 — 9 Healthy mice 177 —

Example 4B Cancer of the Skin

This section relates to a mouse model of skin cancer. The bacterial vaccines used in this experiment were as follows: Streptococcus pneumoniae [cells and broth] vaccine (lot #J049-1 [2×10⁹ ]; Klebsiella pneumoniae [cells and broth] vaccine (lot #J046-1 [2×10⁹ ]; Staphylococcus aureus [cells and broth] vaccine (lot #J041-2 [10×10⁹ ]; Escherichia coli (colon isolate) [cells and broth] vaccine (lot #J047-1 [6×10⁹ ]; Salmonella enterica [cells and broth] vaccine (lot #J31 [15×10⁹ ]; Staphylococcus aureus [cells only] vaccine (lot #J041-2 [10×10⁹]; and media only (S. aureus media) (lot #J041-1). Mice were treated in accordance with the experimental groupings defined in Table 14.

TABLE 14 Experimental Groupings for Skin Cancer Mouse Model B16 melanoma s.c. 2x10e5 cells/ s.c. injection dose schedule 0.1 mL Day: −10, −8, −6, −4, −2, +2, +4, Group Mice Day 0 Vaccine +6, +8, +10, +12, +14, +16, etc. AB1   AB2 8   8

S. pneumoniae [cells and broth] K. pneumoniae [cells and broth] 300x10e6 CFUs/150 μl/mouse 150x10e6 CFUs/75 μl/mouse AB3 8 S. aureus [cells and broth] 1x10e9 CFUs/100 μl/mouse AB4 8 E. coli (colon) [cells and 0.9x10e9 CFUs/150 broth] μl/mouse AB5 8 S. enterica [cells and 1.5 x10e9 CFUs/100 broth] μl/mouse AB6 8 S. aureus [cells only] 1x10e9 CFUs/100 μl/mouse ABC7 12 Media only (S. aureus 100 μl/mouse media) (control)

Specifically, groups of mice were pre-treated sub-cutaneously with bacterial vaccines on days −10, −8, −6, −4, and −2. On day 0, mice were challenged intravenously with a dosage of 2×10e6 of B16 melanoma cells (lot #3995448; ATCC CRL-6323). Thereafter, the mice were treated sub-cutaneously with vaccine injections every second day for the duration of the experiment as defined in Table 14. A control group was treated with media only. Animal weights were measured and recorded every 4 days. Once tumours were palpable, the tumour diameters were measured every second day using callipers. When mice started showing morbidity, or tumour diameters reached 20 mm in any group, the experiment was terminated. Thereafter, all mice were humanely sacrificed. The average volumes of the tumours present in the groups of mice described herein are illustrated in FIG. 15.

Example 4C Cancer of the Colon

This section relates to a mouse model of colon cancer. The bacterial vaccines used in this experiment were as follows: Streptococcus pneumoniae [cells and broth] vaccine (lot #J049-1 [2×10⁹ ]; Klebsiella pneumoniae [cells and broth] vaccine (lot #J046-1 [2×10⁹ ]; Staphylococcus aureus [cells and broth] vaccine (lot #J041-2 [10×10⁹ ]; Escherichia coli (colon isolate) [cells and broth] vaccine (lot #J047-1 [6×10⁹ ]; Escherichia coli (prostate isolate) [cells and broth] vaccine (lot #J040-2 [6×10⁹ ]; Salmonella enterica [cells and broth] vaccine (lot #J31 [15×10⁹]; and media only (E. coli media) (lot #J040-1). Mice were treated in accordance with the experimental groupings defined in Table 15.

TABLE 15 Experimental Groupings for Colon Cancer Mouse Model MC-38 s.c. injection dose colon i.p. schedule Day: −10, −8, 2x10e5 −6, −4, −2, +2, +4, +6, +8, Group Mice Day 0 Vaccine +10, +12, +14, +16, etc. 1AB   2AB 8   8

S. pneumoniae [cells and broth] K. pneumoniae [cells and broth] 300x10e6 CFUs/150 μl/mouse 150x10e6 CFUs/75 μl/mouse 3AB 8 S. aureus [cells and 1x10e9 CFUs/100 μl/ broth] mouse 4AB 8 E. coli [cells and 0.9x10e9 broth] CFUs/150 μl/mouse 5AB 8 E. coli (prostate) 0.9x10e9 [cells and broth] CFUs/150 μl/mouse 6AB 8 S. enterica [cells and 1.5x10e9 broth] CFUs/100 μl/mouse 7ABC 12 Media only (E. coli 150 μl/mouse media) (control)

Specifically, groups of mice were pre-treated sub-cutaneously with bacterial vaccines on days −10, −8, −6, −4, and −2. On day 0, mice were challenged intraperitoneally with a dosage of 2×10e5 MC-38 collo adenocarcinoma cells (gift from Dr. Jeff Schlom Lab, NCI). Thereafter, the mice were treated sub-cutaneously with vaccine injections every second day for the duration of the experiment as defined in Table 15. A control group was treated with media only. The mice were observed for the following clinical factors: weight, cold to touch, diarrhea, rapid respiration, closed eyes, decreased movement, piloerection, and convulsions. When a mouse started to show signs of clinical morbidity, the mouse was humanely sacrificed and that day was defined as the day of death. Survival data for this Example is depicted in FIG. 16.

Further, the health versus morbidity/mortality of the mice involved in this Example was calculated on day 29 of the experiment as defined in Table 16.

TABLE 16 Health v. Morbidity/Mortality Group Score** Group Group Health Status Day 29 Vaccine Score 1 7 dead; 1 tumour + ascites S. pneumoniae 2 2 5 dead; 1 tumour + ascites; 1 K. pneumoniae 17 tumour only; 1 healthy 3 4 dead; 2 tumour + ascites; 2 S. aureus 14 tumour only 4 3 dead; 3 tumour only; E. coli (colon 35 2 healthy infection isolate) 5 3 dead; 3 tumour only; E. coli (prostate 35 2 healthy infection isolate) 6 3 dead; 5 healthy S. enterica 50 7 12 dead Control (media only) 0 **healthy = 10 points; tumour only = 5 points; tumour + ascites = 2 points; and dead = 0 points.

TABLE 17 Summary of survival for each mouse group from colon cancer experiments Mice/ MST* Vaccine group (Days) ILS** (%) # Cured P value*** S. pneumoniae 8 27 12 0 0.29  K. pneumoniae 8 36 50 3 0.061 S. aureus 8 30 25 2 0.002 E. coli (colon) 8 35 46 3 0.008 E. coli 8 >78 >100 4 0.001 (prostate) S. enterica 8 >78 >100 5 0.003 Control 12 24 0 0 — *MST—Median survival time **ILS—Increase in life span over control group ***comparison to placebo treated control group Overall Comparison Survival: Log Rank (Mantel Cox) p = 0.001 Breslow (Generalized Wilcoxon) p = 0.003 Tarone-Ware p = 0.002

Example 4 Summary

Skin Model:

There is a marked therapeutic advantage for the group treated with Staph aureus (cells-only). This study demonstrates the effectiveness of a killed S. aureus vaccine for the treatment of skin cancer in a mouse model, consistent with the fact that S. aureus is the most common cause of skin infection in mice. The data are consistent with the use of immunogenic compositions of the invention to slow or inhibit cancer growth. The S. aureus cells-only vaccine (in which media and exotoxins were removed by centrifuging the cells and broth to collect only the cells and then reconstituting with normal saline) was more effective than S. aureus cells and broth vaccine (which contains media and exotoxins). This may be because S. aureus exotoxins inhibit immune function, such as leuocidins that can kill white blood cells. The invention accordingly includes embodiments in which antigenic determinants that are to be used in immunogenic compositions are separated from immunomodulatory compounds produced by a microbial pathogen of interest.

Lung Model:

The data presented in this Example indicate that there was substantial tumour inhibition with the immunogenic composition derived from K. pneumoniae, consistent with the fact that K. pneumoniae is a common cause of lung infection in mice. In mice (but generally not in humans), S. enterica can cause pneumonia, which is consistent with the beneficial effect of this vaccine in the mouse lung model. Unlike humans, for whom S. pneumoniae is a common lung pathogen, S. pneumoniae is relatively rarely a lung pathogen in mice (although S. pneumoniae pneumonia can be induced in mice). E. coli and S. aureus can uncommonly cause lung infection in mice, which is consistent with their mild benefit illustrated herein. This Example demonstrates that killed K. pneumoniae vaccine is remarkably effective for the treatment of cancer of the lungs in mice, particularly embodiments in which the immunogenic composition includes antigens of only the most commonly pathogenic organism (see Group 2 vs. Group 6).

Colon Model:

S. enterica is one of the most common causes of gastrointestinal and intraperitoneal infection in mice, which is consistent with the beneficial effect illustrated herein in the treatment of gastrointestinal and intraperitoneal cancer in mice.

Of the immunogenic compositions used in this Example (i.e., S. enterica, E. coli, S. aureus, K. pneumoniae, S. pneumoniae), S. enterica is the most common g.i./abdominal pathogen in mice. E. coli is the next most common g.i./abdominal pathogen in mice. S. aureus and K. pneumoniae can be found as part of the colonic flora and can cause g.i./abdominal infection, although far less commonly. S. pneumoniae does not cause g.i./abdominal infection. In accordance with this, the S. enterica vaccine is shown to be substantially beneficial in this mouse colon tumour model, E. coli vaccine is shown to be moderately beneficial, S. aureus and K. pneumoniae vaccines are shown to be mildly beneficial and S. pneumoniae vaccine is shown to be of no benefit. In humans, Salmonella species cause g.i. infection and therefore, one would expect S. enterica and other Salmonella vaccines to be helpful for the treatment of colon cancer in humans.

Example 5 Animal Models Example 5A Illustrating the Influence of a Heat Inactivated Klebsiella pneumoniae Antigenic Composition on Monocyte/Macrophage and Dendritic Cell Populations in Mice

The following methods and materials were utilized in this Example:

Mice. C57BL/6 female mice 7-8 weeks of age were ordered from Harlan Labs (Livermore, Calif.) for these studies.

Antibodies and Reagents. The following antibodies were used in this Example: anti-I-A/I-E FITC (MHC Class II; M5/114.15.2); anti-Gr-1 PE (RB6-8C5); anti-CD11b PerCP-Cy5 (M1/70); anti-CD11c APC(N418); anti-CD4 FITC (GK1.5); anti-NK1.1 PE (PK136); anti-CD8a eFluor780 (53-6.7); anti-CD44 APC (IM7). All antibodies were acquired from eBioscience (San Diego, Calif.). Liberase TM and DNAse I was acquired from Roche. All media was from HyClone (Fisher).

Treatment with Antigenic Compositions. Heat killed K. pneumoniae with phenol (KO12 [5.0 OD600 units]) was diluted 1/10 in PBS containing 0.4% phenol and 100 μl was injected subcutaneously on day 0, 2, 4, and 6 into 4 mice. Control mice (n=5) were injected on day 0, 2, 4, and 6 with PBS.

Brochoalveolar Lavage. On day 7 mice were sacrificed and a bronchoalveolar lavage (BAL) was performed by exposing the trachea followed by insertion of a 22 G catheter attached to a 1 ml syringe. 1 ml of PBS was injected into the lungs and removed and placed into a 1.5 ml microcentrifuge tube. The lungs were subsequently washed 3 more times with 1 ml of PBS and the fluid was pooled. The first wash from each mouse was centrifuged at 400×g and the supernatant was frozen for cytokine analysis. The final 3 ml of lavage fluid was centrifuged and the cells were pooled with the cell pellet from the first lavage. The cells were counted and stained with antibodies specific for MHC class II, Ly6G/C, CD11b, and CD11c. After staining the cells were washed and analyzed on a FACS Calibur flow cytometer.

Lung Digestion. After BAL was performed the lungs were placed in 5 ml of RPMI containing 417.5 μg/ml Liberase TL (Roche) and 200 μg/ml DNAse I (Roche). The lungs were then digested at 37° C. for 30 mins. After digestion the lungs were forced through a 70 um cell strainer to create a single cell suspension. The cells were then centrifuged, washed, resuspended in FACS Buffer (PBS with 2% FCS and 5 mM EDTA) and counted. After counting the cells were stained and analyzed by FACS using the same antibodies as for the BAL cells.

Peritoneal Lavage. 1 ml of PBS was injected into the peritoneum of mice using a 1 ml syringe attached to a 25 G needle after BAL. The abdomen was massaged for 1 minute and 0.5 ml of PBS was recovered from the peritoneum using a 1 ml pipet. The lavage fluid was put in a 1.5 ml centrifuge tube, centrifuged at 400×g for 5 mins, and resuspended in FACS buffer prior to staining and FACS analysis.

Spleen and Lymph Node Analysis. The spleen and draining lymph node were removed after BAL and peritoneal lavage and placed in PBS. The spleen was disrupted by mashing through a 70 μm cell strainer (Fisher) and the lymph node was disrupted using the rubber end of the plunger from a 1 ml syringe. After disruption, the single cell suspension from the spleen and lymph nodes was centrifuged, washed once with FACS Buffer, and resuspended in FACS Buffer prior to counting, staining, and FACS analysis.

FACS Analysis. Cells were stained on ice for 20 mins in 96 well plates using 50 ul of antibodies diluted in FACS buffer. After 20 mins, 100 μl of FACs buffer was added to the wells and the plates were centrifuged at 400×g for 5 mins. Subsequently the media was removed and the cells were washed 1 more time with FACS buffer. After the final wash the cells were resuspended in 200 μl of FACS buffer and the data was acquired using a FACS Calibur flow cytometer (BD). A minimum of 20,000 live events were collected for all samples except the BAL where a minimum of 5,000 events was collected.

The following results were obtained in this Example.

Normal mice without tumours were treated with a K. pneumoniae antigenic composition on day 0, 2, 4, and 6. On day 7 the mice were sacrificed and the bronchoalveolar lavage fluid, lung tissue, peritoneal lavage fluid, lymph nodes, and spleen was analyzed for changes in monocyte and macrophages. An increase in the number of acute inflammatory blood monocytes/macrophages, defined by high expression of CD11b and Gr-1 (same marker as Ly6c), and F4/80 in the lymph node draining the site of injection of the K. pneumoniae antigenic composition was observed (see: FIG. 17A). These acute inflammatory monocytes/macrophages also express very high levels of MHC class II molecules suggesting exposure to bacterial antigens. Importantly, treatment of mice with the K. pneumoniae antigenic composition for one week led to a marked increase in the frequency of acute inflammatory monocytes in the bronchoalveolar lavage fluid and in the lungs (i.e., the targeted organ) but not in the spleen or peritoneum of treated mice, suggesting that treatment can induce homing of monocytes specifically to the lungs without affecting other organs (see: FIG. 17B). Monocytes can differentiate into dendritic cells (DCs) in the lungs and consistent with our observations of a marked increase in monocyte recruitment it was also observed that there was a marked increase in the frequency of cells displaying markers for mature DCs (see: FIG. 17C).

As illustrated in FIG. 17, treatment with a K. pneumoniae antigenic composition for 7 days resulted in a marked increase (compared to treatment with placebo=PBS) in both acute inflammatory monocytes and dendritic cells in the lungs of mice. As illustrated in FIG. 17, mice were treated with either a K. pneumoniae antigenic composition for or PBS on day 0, 2, 4, and 6. On day 7, the mice were sacrificed and the total number of A) and B) inflammatory monocytes (CD11b+ Gr-1+ cells) and C) dendritic cells (CD11c+ MHC class II+ cells) were determined by flow cytometry in the lung and spleen. The error bars depicted in A) represent the mean of 4-5 mice per group.

Example 5B Illustrating the Influence of a Heat Inactivated Klebsiella pneumoniae Antigenic Composition and a Heat Inactivated E. Coli Antigenic Composition on Monocyte/Macrophage, Dendritic Cell, and Effector Cell Populations in Mice

The following methods and materials were utilized in this Example:

Mice. C57BL/6 female mice 7-8 weeks of age were ordered from Harlan Labs (Livermore, Calif.) for these studies.

Antibodies and Reagents. The following antibodies were used: anti-I-A/I-E FITC (MHC Class II; M5/114.15.2); anti-Gr-1 PE (RB6-8C5); anti-CD11b PerCP-Cy5 (M1/70); anti-CD11c APC(N418); anti-CD4 FITC (GK1.5); anti-NK1.1 PE (PK136); anti-CD8a eFluor780 (53-6.7); anti-CD44 APC (IM7). All antibodies were acquired from eBioscience (San Diego, Calif.). Liberase TM and DNAse I was acquired from Roche. All media was from HyClone (Fisher).

Treatment with Antigenic Compositions. Heat-killed K. pneumoniae with phenol (K. pneumoniae; lot KO12; 5.0 OD600 units) was diluted 1/10 in PBS containing 0.4% phenol and 100 ul was injected subcutaneously on day 0, 2, 4, and 6 into 5 mice. Heat-killed E. coli (lot; 5.0 OD600 units) was diluted 1/10 in containing 0.4% phenol and 100 μl was injected subcutaneously on day 0, 2, 4, and 6 into 5 mice. Control mice (n=5) were injected on day 0, 2, 4, and 6 with PBS.

Brochoalveolar Lavage. On day 7 mice were sacrificed and a bronchoalveolar lavage (BAL) was performed by exposing the trachea followed by insertion of a 22 G catheter attached to a 1 ml syringe. 1 ml of PBS was injected into the lungs and removed and placed into a 1.5 ml microcentrifuge tube. The lungs were subsequently washed 3 more times with 1 ml of PBS and the fluid was pooled. The first wash from each mouse was centrifuged at 400×g and the supernatant was frozen for cytokine analysis. The final 3 ml of lavage fluid was centrifuged and the cells were pooled with the cell pellet from the first lavage. The cells were counted and stained with antibodies specific for MHC class II, Ly6G/C, CD11b, and CD11c. After staining the cells were washed and analyzed on a FACS Calibur flow cytometer.

Lung Digestion. After BAL was performed the lungs were placed in 5 ml of RPMI containing 417.5 μg/ml Liberase TL (Roche) and 200 μg/ml DNAse I (Roche). The lungs were then digested at 37° C. for 30 mins. After digestion the lungs were forced through a 70 μm cell strainer to create a single cell suspension. The cells were then centrifuged, washed, resuspended in FACS Buffer (PBS with 2% FCS and 5 mM EDTA) and counted. After counting the cells were stained and analyzed by FACS using the same antibodies as for the BAL cells.

Peritoneal Lavage. 1 ml of PBS was injected into the peritoneum of mice using a 1 ml syringe attached to a 25 G needle after BAL. The abdomen was massaged for 1 minute and 0.5 ml of PBS was recovered from the peritoneum using a 1 ml pipet. The lavage fluid was put in a 1.5 ml centrifuge tube, centrifuged at 400×g for 5 mins, and resuspended in FACS buffer prior to staining and FACS analysis.

Spleen and Lymph Node Analysis. The spleen and draining lymph node were removed after BAL and peritoneal lavage and placed in PBS. The spleen was disrupted by mashing through a 70 μm cell strainer (Fisher) and the lymph node was disrupted using the rubber end of the plunger from a 1 ml syringe. After disruption, the single cell suspension from the spleen and lymph nodes was centrifuged, washed once with FACS Buffer, and resuspended in FACS Buffer prior to counting, staining, and FACS analysis.

FACS Analysis. Cells were stained on ice for 20 mins in 96 well plates using 50 μl of antibodies diluted in FACS buffer. After 20 mins, 100 μl of FACs buffer was added to the wells and the plates were centrifuged at 400×g for 5 mins. Subsequently the media was removed and the cells were washed 1 more time with FACS buffer. After the final wash the cells were resuspended in 200 μl of FACS buffer and the data was acquired using a FACS Calibur flow cytometer (BD). A minimum of 20,000 live events were collected for all samples except the BAL where a minimum of 5,000 events was collected.

The following results were obtained in this Example:

As illustrated in FIG. 18, mice were treated on day 0, 2, 4, and 6 with either a K. pneumoniae antigenic composition, an E. coli antigenic composition or PBS. On day 7 the mice were sacrificed and the total number of inflammatory monocytes (CD11b+ Gr-1+ cells) and dendritic cells (CD11c+ MHC class II+ cells) were determined by flow cytometry in the peritoneal lavage fluid, lungs, lymph node and spleen. Error bars in FIG. 18 represent the standard deviation from 5 mice. *p-value<0.05 using a Student's t-test.

FIG. 18 illustrates that treatment with a K. pneumoniae antigenic composition, but not an E. coli antigenic composition treatment, markedly increased the number of monocytes and DCs in the lungs of mice. In contrast to the lungs, K. pneumoniae did not lead to an increase in monocytes in the peritoneum of the mice whereas E. coli did. Importantly, there was only a slight increase in the number of inflammatory monocytes and no increase in DCs in the spleens of mice treated with either K. pneumoniae or E. coli suggesting that the effects of the therapies are not general and are, in fact, specific for a particular organ site. In addition to looking at the effects of treatment on inflammatory monocytes and DCs in the lungs of mice, we also looked at changes in other leukocytes such as cytotoxic CD8 T cells, CD4 T helper cells, and natural killer (NK) cells all of which can potentially play a role in anti-tumour immunity.

FIG. 19 illustrates that a K. pneumoniae antigenic composition, but not PBS or an E. coli antigenic composition, resulted in a marked increase in the frequency and total numbers of NK cells, CD4 and CD8 T cells in the lungs of treated mice. This Example is the first demonstration to our knowledge that subcutaneous injection of a killed bacterial species which normally causes lung infection can promote the accumulation of leukocytes in the lungs without the presence of any inflammation in that site. In addition, we have demonstrated that this effect is specific to the targeted site and that it is also specific to the bacterial constituents of the treatment used.

As illustrated in FIG. 19, mice were treated on day 0, 2, 4, and 6 with either a K. pneumoniae antigenic composition, an E. coli antigenic composition, or PBS. On day 7, the mice were sacrificed and the total number of CD4 T cells, CD8 T cells, and natural killer (NK) cells were determined by flow cytometry. Error bars represent the sd of values obtained from 5 mice per group. *p-value<0.05 using a Student's t-test.

Example 5C Illustrating the Effects of Heat and Phenol Inactivated Klebsiella pneumoniae (K. pneumoniae) Antigenic Compositions on Anti-Tumor Response in Mice, and the Status of Inflammatory Monocytes and Dendritic Cells Following Treatment in Tumor-Bearing Mice

The following methods and materials were utilized in this Example:

Tumour Cell Inoculations. The Lewis lung carcinoma cell line derived from the C57BL/6 background were acquired from ATCC (Manassas, Va.). The cells were maintained in Dulbecco's Modified Eagles Media (ATCC, Manassas, Va.) containing 10% FCS. The cells were grown in a humidified 37° C. incubator with 5% CO₂. Prior to tumour inoculation, cells were detached from culture plates using 0.25% trypsin and 0.53 mM EDTA. The cells were washed in PBS and resuspended at 8×10⁶ cells/ml and 200 ul (4×10⁵ cells) was injected intravenously into mice.

Treatment with Antigenic Composition. The following antigenic compositions were used in this study: a heat-inactivated K. pneumoniae antigenic composition with phenol (lot KO12) and a phenol-inactivated K. pneumoniae antigenic composition (lot KO25). Both heat-inactivated K. pneumoniae and phenol-inactivated K. pneumoniae are concentrated to 5.0 OD600 units. 0.1 ml of K. pneumoniae diluted 1/10 in PBS with 0.4% phenol was injected subcutaneously every 2 days starting on day 2 after tumour injection.

Analysis of Inflammatory Monocytes, DCs, T Cells, and NK Cells.

All analysis was done according to the methods used in Example 5B above.

TABLE 18 Experimental groupings and dose schedule for Example 5C LL/2 Tumor Site of Concentration cells LL/2 of K. Pneumoniae Schedule Injection Number of and Tumor (OD units) of Volume Date of Group animals/sex dose Injection Treatment Injections Treatment (ml) Sacrifice 1A 5F 4 × 10⁵ Intravenous DPBSWP¹ None Once daily 0.1 Day 9  2A 5F LL/2 HKWP² 0.05 on day 2, 3A 5F PHWP³ 0.05 4, 6, and 8 1B 5F DPBSWP¹ None Once daily Day 16 2B 5F HKWP² 0.05 on day 2, 3B 5F PHWP³ 0.05 4, 6, 8, 10, 12, 14, 1C 5F DPBSNP¹ None Once daily Day 23 2C 5F HKWP² 0.05 on day 2, 3C 5F PHWP³ 0.05 4, 6, 8, 10, 12, 14, 16, 18, 20, 22 ¹Dulbecco's Phosphate Buffered Saline with phenol ²Heat killed with phenol ³Phenol killed with phenol

The following results were obtained in this Example:

This example was designed to determine if the presence of tumour impacted the recruitment of cells to the lungs and whether the treatment effect increases over time resulting in further increases in cell recruitment with ongoing treatment and thus, potentially, more optimal therapeutic effect with prolonged treatment. In addition, we wanted to determine whether a K. pneumoniae antigenic composition inactivated by phenol was more effective than a K. pneumoniae antigenic composition inactivated by heat.

FIG. 20 clearly demonstrates that by day 9 (i.e., 4 treatments with a K. pneumoniae antigenic composition) there is already a marked increase in the number of acute inflammatory monocytes, DCs, T cells, and NK cells in the lungs of mice treated with a K. pneumoniae antigenic composition inactivated by heat or phenol, many times greater than that of the lungs of mice treated with placebo (normal saline=PBS), again, clearly demonstrating the marked targeted cellular immune response in the lungs triggered by K. pneumoniae antigenic composition therapy. On day 9, there was a suggestion that phenol inactivation was more effective than heat inactivation, but this trend reversed by day 16. Importantly, however, with reference to the cell numbers in the lungs on day 9 and day 16, it is evident that there is a cumulative effect of bacterial treatment on the recruitment of cells to the lungs. For example in the group treated with a phenol inactivated K. pneumoniae antigenic composition there are about 100,000 acute inflammatory monocytes in the lungs of the mice at day 9 and this number increases substantially to 400,000 by day 16, demonstrating a substantially increasing response with ongoing treatment. The same increased treatment response with ongoing treatment occurred in mice treated with heat inactivated bacteria. Importantly, this cumulative treatment effect is observed for all other cell types analyzed as well. In this study, there was no demonstrable statistically significant difference in immune cell recruitment with heat or phenol inactivated K. pneumoniae antigenic compositions.

As illustrated in FIG. 20, mice were injected with 4×10⁵ lewis lung carcinoma cells intravenously on day 0. The mice were subsequently treated every other day starting on day 2 with a K. pneumoniae antigenic composition generated by heat inactivation, or phenol inactivation, or with PBS. On day 9 and day 16 the mice were sacrificed and the total numbers of (A) inflammatory monocytes (CD11b+ Gr-1+) and DCs (CD11c+ lab+) or (B) CD4 T cells, CD8 T cells, and natural killer (NK) cells were determined by flow cytometry. Bars represent respectively: the PBS treated group, the mice treated with a heat-inactivated K. pneumoniae antigenic composition and mice treated with a phenol-inactivated K. pneumoniae antigenic composition. Error bars represent the sd of values obtained from 5 mice per group. *p-value<0.05 using a Student's t-test.

The results of this study demonstrate an increasing immune response within the targeted tissue with ongoing treatment.

Example 5D Illustrating the Effects of Heat, Irradiation, and Phenol Inactivation on K. Pneumoniae Antigenic Compositions, Including Leukocyte Recruitment into the Lungs of Mice, and the Effects of Phenol as a Preservative has any Effects

The following methods and materials were utilized in this Example:

Mice. C57BL/6 female mice 7-8 weeks of age were ordered from Harlan Labs (Livermore, Calif.) for these studies.

Antigenic Compositions. Heat killed K. pneumoniae antigenic composition with phenol (KO12), heat killed K. pneumoniae antigenic composition without phenol (KO25), irradiated K. pneumoniae antigenic composition without phenol (KO24), and phenol killed K. pneumoniae antigenic composition without phenol (KO25) were used in this study. All bacterial formulations were at a concentration of 5.0 OD units in saline. For 1/10 dilution, 1 ml of bacterial formulation was added to 9 ml of DPBS and mixed immediately and then again prior to injection. For 1/100 dilution, 0.1 ml of bacterial formulation will be added to 9.9 ml of DPBS and mixed immediately and then again prior to injection. For dilutions of heat-killed Klebsiella pneumoniae antigenic composition with phenol, the dilutions were carried out as above using a DPBS solution containing 0.4% phenol (w/v). To prepare the 0.4% phenol in DPBS, first a 5% phenol solution was prepared by adding 0.5 g of solid phenol (Sigma Aldrich, St. Louis, Mo.) to 10 ml of DPBS (Hyclone, Logan, Utah) This solution was filtered through a 0.22 um filter (Millipore, Billerica, Mass.) and stored at 4° C. Immediately prior to use the 5% phenol solution was diluted 1 ml in 12.5 ml DPBS and used to prepare the bacterial formulations.

Treatment with Antigenic Compositions. 5 mice per group were treated subcutaneously on day 0, 2, 4, and 6 with 0.1 ml of a heat-killed K. pneumoniae antigenic composition diluted 1/10 in PBS or PBS with 0.4% phenol, 0.1 ml of an irradiated K. pneumoniae antigenic composition diluted 1/10 in PBS, or a phenol inactivated K. pneumoniae antigenic composition diluted 1/10 with PBS or PBS with 0.4% phenol. On day 7 the mice were sacrificed and leukocyte recruitment to the lungs was analyzed as in Example 5B.

The following results were obtained in this Example:

In this example, we used leukocyte recruitment to the lungs as a surrogate of efficacy to compare the efficacy of K. pneumoniae antigenic compositions inactivated by various methods. FIG. 21 illustrates that, for both heat killed and phenol killed K. pneumoniae antigenic compositions, the addition of phenol (0.4%) as a preservative, increased efficacy, as measured by cellular recruitment. In some embodiments, a small amount of phenol (i.e., 0.4% as a preservative) may stabilize a component of the bacterial cell wall, for example a component that is important in antigen pattern recognition and activating an optimal targeted response. In comparing the 3 formulations containing phenol as a preservative (i.e., heat killed, phenol killed and radiation killed), irradiated K. pneumoniae antigenic composition led to the greatest recruitment of acute inflammatory monocytes, DCs, NK cells, and T cells to the lungs, followed by phenol killed K. pneumoniae antigenic composition, with heat killed K. pneumoniae antigenic composition resulting in the least cellular recruitment.

As illustrated in FIG. 21, mice were treated on day 0, 2, 4, and 6 with K. pneumoniae antigenic composition inactivated by heat (HKWP) or without (HKnp) phenol preservative, inactivated with phenol with (PKWP) or without (PKnp) phenol preservative, or K. pneumoniae antigenic composition inactivated by irradiation with phenol preservative (IRWP). On day 7 the mice were sacrificed and the total numbers of (A) inflammatory monocytes (CD11b+ Gr-1+) and DCs (CD11c+ lab+) or (B) CD4 T cells, CD8 T cells, and natural killer (NK) cells were determined by flow cytometry. Error bars represent the sd of values from 5 mice per group. *p-value<0.05 compared to mice treated with IRWP using a Student's t-test.

Example 6 Clinical Studies Involving Advanced Epithelial Cancers

Overview of Treatment

The following patients with different advanced cancers have undergone treatment with heat inactivated targeted bacterial antigenic compositions. Fully informed written consent was received for each patient and in every case. The treatment consisted of repeated (3×/week) subcutaneous injections of exact amounts of the vaccine in the abdominal region. The dosage was gradually increased in each patient to achieve a sufficient skin response (3-5 cm redness lasting for ca. 24 h). For each patient a case report form (CRF) documented skin reaction and possible clinical effects and/or side effects related to the treatment. Characteristic and concomitant treatments as well as the response to therapy of the patients are briefly described.

Patient #1:

53y old male patient with advanced melanoma, ICD10: C43, 1st diagnosed November 2005 lesion under right big toe nail, histology one year later December 2006: advanced malignant melanoma; patient refused amputation of the big toe; May 2008 lymphatic metastasis to the right leg, at the time of first presentation for targeted bacterial antigenic composition treatment (September 2008) leg swollen with 100% increase in circumference: Karnofsky 80%, no pretreatment.

Treatments Over 6 Month September 2008-April 2009:

-   -   12×intraperitoneal Ozone (O3) insufflation;     -   42×locoregional radiofrequency hyperthermia (13.56 Mhz);     -   18×moderate whole body hyperthermia 38.5° C.;     -   6 month treatment with Staph. aureus antigenic composition s.c.;     -   Orthomolecular medicine: high dose vitamin C infusions (0.5         g/kg/BW), Vitamin D3; 2.000 iu/day, Artesunate 200 mg/day,         Celebrex 100 mg/day, low dose naltrexone, medical; mushroom         (cordyceps, reishi, shitake), selenium 200 uc/day, curcumin         3.000 mg/day, proteolytic enzymes (Wobemugos)

Epicrisis Details:

-   -   PET July 2008: SUV in right big toe 4.81, knee: 5.01     -   PET December 2008: SUV in right big toe 3.80, knee: 4.02     -   We started treatment end of September 2008.     -   At that time (September 2008) there were clinically already         lymph nodes in the groin palpable which were not seen on the PET         from July 2008.     -   May 2010: good clinical condition, PET confirms complete         remission, Karnofsky 100%.         Patient #2:

48y old female patient with advanced bilateral breast cancer, ICD10: C50.9 1st diagnosed April 2008; histology ductal infiltrating adenocarcinoma of the breast, ER/PR pos., Her2 not known, T1/T2, N1 (sentinel node axilla), M0 G3; multiple treatments with sodium bicarbonate injections and repeated surgery to both breasts; patient refused the proposed bilateral mastectomy and was never resected “in sano” (e.g., margins of the lumpectomies were never free of tumor cells). Patient also refused Chemotherapy and/or hormone therapy. Karnofsky 90%, no pretreatment.

Treatments Over 8 Month March 2009-November 2009:

-   -   3×autologous Dendritic cell therapy in combination with:     -   3×long-duration moderate whole body hyperthermia 40° over 8 h     -   57×locoregional radiofrequency hyperthermia to both breasts         (13.56 Mhz)     -   6 month treatment with Staph. aureus antigenic composition s.c.     -   Orthomolecular medicine: high dose vitamin C infusions (0.5         g/kg/BW), low dose naltrexone, medical mushroom (cordyceps,         reishi, shitake), curcuma 3.000 mg/day, zinc

Epicrisis Details:

-   -   Treatment started end of March 2009.     -   May 2010: bilateral breast MRI shows no abnormality detected,         good clinical condition, Karnofsky 100%         Patient #3:         73y old female patient with advanced NSCLC cancer FIGO IIc,         ICD10: C34, 1st diagnosed June 2009; histology clear cell         adenocarcinoma of the lungs, T4, N1, M0 G3; she underwent         neoadjuvant CHT; the restaging after 3 cycles neoadjuvant CHT         demonstrated T2 tumor; she then underwent left pneumectomy R0         resection and mediastinal lymphadenectomy; Karnofsky 90%.

Treatments Over 7 Month August 2009-March 2010:

-   -   August 2009 Began chemotherapy with Taxan/Cisplatin until         October 2009 in combination with:     -   4×long-duration moderate whole body hyperthermia 40° over 8 h         (January-February 2009)     -   20×locoregional radiofrequency hyperthermia to the thorax (13.56         Mhz) (August-October 2009)     -   October 2009 le Pneumectomy R0 resection (Oncology decided         against further adjuvant CHT)     -   6 month treatment with Klebsiella pneumoniae antigenic         composition s.c. (August 2009-February 2010)     -   Orthomolecular medicine: thymus peptides i.m., indometacin,         cimetidine, high dose vitamin C infusions (0.5 g/kg/BW), ALA/N         protocol (low dose naltrexone and alpha lipoic acid), medical         mushroom (reishi), curcuma 3.000 mg/day, zinc, melatonin,         inhalation of ionized oxygen

Epicrisis Details:

-   -   Started treatment end of August 2009.     -   May 2010: CT Thorax and Tumor marker CEA, NSE and CYFRA show         complete remission, good clinical condition, Karnofsky 100%.         Patient #4:

50y old female patient with advanced Breast cancer, ICD10: C50, with disseminated hepatic and pulmonary metastasis, 1st diagnosed August 1990; histology undifferentiated cirrhoses type adenocarcinoma of the breast, pT1c, N1, M0 G3; she underwent multiple chemotherapy courses over 20 years; November 2004 first scar reoccurrence, December 2004 ablation left breast, 6×CHT Epitax and radiation of thoracic wall; September 2005 1st diagnosis of disseminated liver and pulmonary metastases: again 8×CHT with Epitax until March 2006. Restaging showed progressive disease at which time she began targeted bacterial antigenic composition treatment. Karnofsky 90%.

Treatments Over 4 Years March 2006-March 2010:

-   -   March 2006 Began treatment with Polyvaccinum forte vaccine in         combination with:     -   3×autologous Dendritic cell therapy in combination with         (June-August 2006):     -   3×long-duration moderate whole body hyperthermia (LD-WBH) 40°         over 8 h (January-February 2009)     -   25×locoregional radiofrequency hyperthermia to the thorax &         liver (13.56 Mhz) (March-June 2006)     -   8 month treatment with Klebsiella pneumoniae antigenic         composition (November 2008-July 2009)     -   October 2009 TM CEA and CA15/3 started rising again     -   February-March 2009 2× autologous Dendritic cell therapy without         LD-WBH     -   April 2010 thermal ablation of liver mets (No change of lung         metastasis)     -   Orthomolecular medicine: thymus peptides i.m., indometacin,         cimetidine, high dose vitamin C infusions (0.5 g/kg/BW), curcuma         3.000 mg/day, zinc, proteolytic enzymes

Epicrisis Details:

-   -   We started treatment end of March 2006.     -   May 2006: CT Thorax show stable disease over 4 years,         progressive disease of liver mets, good clinical condition,         Karnofsky 100%.         Patient #5:

66y old male patient with advanced prostate cancer, ICD10: C61, with disseminated bone and lymphatic metastasis, 1st diagnosed January 1997; histology undifferentiated adenocarcinoma of the prostate, pT3, N1, M1 G3; he underwent multiple Hormone- and CHT over 13 years; patient is in good clinical condition surviving metastatic prostate cancer for 13 years since diagnosis; Karnofsky 90%.

Treatments Over 11 Years November 1999-May 2010:

-   -   13 years anti-androgen with Suprefact, Zoladex, Casodex,         Trenantone, Estracyt, β-Sitosterol     -   June 2006-December 2007 Began Mixed bacterial vaccine treatment         with Polyvaccinum forte vaccine     -   Since March 2008 regular chemotherapy with Taxotere 140 mg every         3-4 weeks     -   50×moderate whole body hyperthermia 39° over 3 h (1999-2009)     -   18 month treatment with Staph. aureus antigenic composition         (November 2008-May 2010, ongoing)     -   May-June 2009 2× autologous Dendritic cell therapy without         moderate WBH 39°, 3 h     -   Orthomolecular medicine: wheat grass, cimetidine, Zometa, high         dose vitamin C infusions (0.5 g/kg/BW), curcuma 3.000 mg/day,         boswellia serrata (Indian) 400 mg 4×4/day, zinc, proteolytic         enzymes

Epicrisis Details:

-   -   We started treatment end of 1999.     -   May 2010: Bone scan shows stable disease; PSA currently 89         ng/ml, good clinical condition, Karnofsky 90%.         Patient #6:

52y old female patient with advanced primary cancer of the peritoneum, ICD10: C48.2, with disseminated peritoneal carcinosis, 1st diagnosed June 2003; histology undifferentiated adenocarcinoma of the peritoneum, pT3, N1, M1 G3; she underwent Debulking OP with ovarectomy bilaterly and hysterectomy and adjuvant chemotherapy with Taxol/Paraplatin: progressive disease and change to Taxol/Paraplatin with SD until August 2008; progressive disease with disseminated peritoneal LK metastasis and 3rd line CHT with Carboplatin and beginning of treatment with targeted bacterial antigenic composition; patient was in good clinical condition; Karnofsky 100%.

Treatments Over 4 Month May-September 2009:

-   -   5× Carboplatin chemotherapy (3rd line) followed by:     -   5×long-duration moderate whole body hyperthermia (LD-WBH) 40°         over 8 h (May-September 2009)     -   20×locoregional radiofrequency hyperthermia to the abdomen         (13.56 Mhz) (May-September 2009)     -   2 month treatment with E. coli (colon) antigenic composition         (May-July 2009)     -   Orthomolecular medicine: high dose vitamin C infusions (0.5         g/kg/BW), high dose artichoke and sylimarin extracts (liver)

Epicrisis Details:

-   -   We started treatment end of May 2009.     -   April 2010: CT abdomen and tumour marker demonstrate complete         remission; good clinical condition, Karnofsky 100%         Patient #7:

50y old female patient with inoperable pancreatic cancer, ICD10: C25.9, with the cancer infiltrating the large vessels; Sonographic and CT evidence suggested invasion into superior mesenteric vein. first diagnosed February 2009; histology undifferentiated adenocarcinoma of the pancreas, pT3, N1, M1 G3 with peritoneal carcinosis; she underwent local radiation and low dose Xeloda as radiation sensitizer; when she began treatment at our clinic the cancer was still unresectable; Karnofsky 100%.

Treatments Over 2 Month June-July 2009: (E. Coli SSI for 11 Months)

-   -   1×autologous NDV-primed Dendritic cell therapy in combination         with:     -   1×long-duration moderate whole body hyperthermia 40° over 8 h         (July-October 2009)     -   4×moderate whole body hyperthermia 38.5°     -   15×locoregional radiofrequency hyperthermia to the abdomen         (13.56 Mhz) (June-July 2009)     -   11 months treatment with E. coli (colon) antigenic composition         (June 2009 until today, ongoing)     -   Orthomolecular medicine: thymus peptides i.m; medical mushroom         (reishi, cordyceps, shitake;) high dose vitamin C infusions (0.5         g/kg/BW), high dose proteolytic enzyme therapy (wobenzym         phlogenzym), cimetidine.

Epicrisis Details:

-   -   We started treatment end of June 2009.     -   May 2010: complete remission, NED; PET February 2010         demonstrated no glucose uptake; tumour marker normal CA19/9: 4;         good clinical condition, Karnofsky 100%

Example 7 Dosage Studies (QB28 Study)

In an effort to examine the role of dosing, mice were treated with either different doses of K. pneumoniae antigenic composition or a PBS control. All mice (C57BL/6) began treatment with K. pneumoniae_antigenic composition or PBS on day −10, −8, −6, −4 and −2 using the following injection sites (1^(st) injection: ventral inguinal right; 2^(nd) injection: ventral axillary right, 3^(rd) injection: ventral axillary left; 4^(th) injection: ventral inguinal left etc.). All mice then received a tumor inoculation dose of 3×10⁵ Lewis Lung carcinoma cells via intravenous injection into the lateral tail vein of the mice. The doses of antigenic compositions or PBS were as follows: i) PBS 0.1 ml; ii) K. pneumoniae 0.1 mL of OD600=1.67; iii) K. pneumoniae 0.1 mL of OD600=0.5. Mice received K. pneumoniae antigenic compositions or PBS, treatment on days 2, 4, 6, and 8. The experiment was termination on day 10; all mice were sacrificed, their lungs were surgically removed, rinsed in water, weighed, and then placed into Bouins fluid for fixation and counting 24 hours later. As shown in FIG. 22, each data point represents the number of tumour nodules from one mouse. Photographs of representative lungs from these experiments are shown in FIG. 23. FIG. 23 shows that the lungs from mice treated with the PBS control show significant numbers of nodules. By way of comparison, FIG. 23 demonstrates that the lungs from mice treated with K. pneumoniae antigenic composition shows fewer numbers of nodules at a rate equivalent to those shown in FIG. 22.

QB30 Study. In further studies on the effect of dosage of K. pneumoniae antigenic compositions, it was demonstrated that if a dosage of a K. pneumoniae antigenic composition is too low, it is not effective for the treatment of lung cancer. In these studies, the results of which are shown in FIG. 24, all mice (C57BL/6) began treatment with K. pneumoniae antigenic composition or PBS on day −10, −8, −6, −4 and −2 using the following injection sites (1^(st) injection: ventral inguinal right; 2^(nd) injection: ventral axillary right, 3rd injection: ventral axillary left; 4^(th) injection: ventral inguinal left etc.). All mice then received a tumor inoculation dose of 3×10⁵ Lewis Lung carcinoma cells via intravenous injection into the lateral tail vein of the mice. The doses of antigenic compositions or PBS was as follows: i) PBS 0.1 ml; ii) K. pneumoniae 0.1 mL of OD600=0.5; iii) K. pneumoniae 0.1 mL of OD600=0.05. Mice continued to receive K. pneumoniae antigenic compositions, or PBS, treatment on day 2, 4, 6, 8, 10, 12, 14, and 16. The experiment was termination on day 18; all mice were sacrificed, their lungs were surgically removed, rinsed in water, weighed, and then placed into Bouins fluid for fixation and counting 24 hours later. As shown in FIG. 24, each data point represents the number of tumour nodules from one mouse.

The results from the QB28 and QB30 studies suggest that extremely high doses of K. pneumoniae antigenic compositions are ineffective, perhaps due to over-stimulation of the host immune system. The results from these studies also suggest that low doses are ineffective, perhaps due to insufficient stimulation of the host immune system.

Example 8 Cisplatin Efficacy Studies

In an effort to examine the role between Cisplatin and chemotherapy and doses of K. pneumoniae antigenic compositions, the QB38 study was completed. Briefly, all mice received a tumor inoculation dose of 3×10⁵ Lewis Lung carcinoma cells via intravenous injection into the lateral tail vein on day 0 of the study. Following this inoculation, all mice were pooled into a single cage and subsequently distributed into their respective cages at random to control against biased data. On the morning of day +2 of this study, mice within the Cisplatin group were injected with 10 mg/kg of this drug intraperitoneally. Control mice were injected with control (PBS). Thereafter, on the afternoon of day +2 of this study, mice received K. pneumoniae antigenic compositions, or PBS; these injections continued on days 4, 6, 8, 10, and 12. The study was terminated on day 14; thereafter, all mice were sacrificed, their lungs were surgically removed, rinsed in water, weighed, and then placed into Bouins fluid for fixation and counting 24 hours later. As shown in FIG. 25, each data point represents the number of tumour nodules from one mouse based on whether the mice were treated with PBS, K. pneumoniae antigenic compositions, K. pneumoniae antigenic compositions combined with Cisplatin, or Cisplatin alone. The results summarized in FIG. 25 indicate that there were fewer nodules in mice treated with K. pneumoniae antigenic compositions and Cisplatin compared with those treated with Cisplatin alone, K. pneumoniae antigenic compositions alone, or the PBS control.

A further study was designed to determine whether K. pneumoniae antigenic composition therapy could work in synergy with platinum-based chemotherapy to extend the survival of mice bearing pulmonary Lewis Lung tumors. Four groups of five C57BL/6 female mice all received 10⁵ Lewis Lung carcinoma cells i.v. on day 0. On day 2, groups 3 and 4 received a single i.p. dose of 10 mg/kg Cisplatin. Beginning on day 4 the mice received either K. pneumoniae or placebo (PBS) every 2 days until death. FIG. 26 illustrates the survival of all of the mice and the table shows the p-values of the various survival curves calculated using the Log-rank Test. Treatment of mice with Cisplatin alone increased the survival of mice with lung tumors with median survival increasing from 16 days in the PBS group to 23 days in the PBS+Cisplatin group. Treatment with K. pneumoniae alone also increased survival of the mice compared to PBS (median survival 19 days for K. pneumoniae vs. 16 days for PBS). Most importantly Cisplatin chemotherapy together with K. pneumoniae therapy had the greatest therapeutic benefit (median survival of 32 days) demonstrating the synergy between platinum-based chemotherapy and antigenic composition therapy in a mouse model of lung cancer. The p-values for the data generated in this QB45 study are shown in Table 19 below.

TABLE 19 Survival Date (QB45) PBS + K. pneumoniae + PBS K. pneumoniae cisplatin cisplatin Median 16 19 23 32 survival (days) P value (to 0.037 0.002 0.002 PBS) P value (to 0.008 PBS + cisplatin)

As shown in this Example, antigenic compositions can be used on the same day as Cisplatin or at a period after Cisplatin administration. As used herein, the term “antigenic composition” refers to a composition that includes antigens of one or more microbial species. As used herein, the term “microbial species” may refer to a viral pathogen or a bacterial pathogen or a fungal pathogen, as detailed herein.

A further study was designed to explore whether there is any synergy between platinum based chemotherapy and K. pneumoniae antigenic composition therapy for the treatment of lung cancer in mice. All of the mice received 10⁵ Lewis Lung carcinoma cells iv on day 0. The mice received antigenic compositions or PBS subcutaneously every 2 days starting on day 0. On day 12, some of the mice were treated with cisplatin (10 mg/kg) intraperitoneally. The following day (day 13), 3 mice from each group were bled and the blood cells were stained with anti-CD11b antibody and analyzed by FACS. The plots in FIG. 27 depict the frequency of CD11b+ myeloid cells in the blood on day 13. Each point represents a single mouse. The results of this study demonstrate that antigenic composition therapy can enhance the frequency of myeloid cells (monocytes, macrophages, granulocytes, dendritic cells) in the blood when given with cisplatin. This may enhance immunity in the animals by providing a greater number of these innate myeloid cells which are capable of responding to the tumors or pathogens. In addition, since bone marrow suppression is a clinically important side-effect of chemotherapy treatment, with resultant reduction in myeloid cells in the blood, which can result in postponement/discontinuation of chemotherapy or susceptibility to infection, the enhancement of myeloid cells with antigenic composition therapy during chemotherapy, may be helpful to reduce the risk of this important and clinically relevant side effect of chemotherapy.

Example 9 Macrophage Studies (MOA13 Study)

To examine the role of macrophages with respect to embodiments of the invention, the MOA13 study was completed. Briefly, mice were either inoculated with 3×10⁵ Lewis Lung carcinoma cells or were injected with HBSS as a vehicle control. For mice inoculated with Lewis Lung carcinoma cells, they were pooled into a single cage where they were subsequently transferred at random to their respective cages. Thereafter, mice were treated with either K. pneumoniae antigenic compositions, or PBS, on days 2, 4, 6 and 8. Thereafter, all mice were sacrificed on day 9. To obtain information with respect to myeloid and NK cell frequencies, 20 mice (5 from each group) had their lungs surgically removed, and the lungs were digested using Liberase TL and DNAse. Following the digesting and cell preparation, a single cell suspension was generated. Thereafter, a portion of the cells were transferred into 96 round bottom plates for staining using myeloid specific antibodies (CD11b+, NK1.1+) and NK specific antibodies (NK1.1+, CD11b+). For the former cell type, gates were used to select only CD11b+ and NK1.1− cell populations. Thereafter, cell data acquisition was performed using BD FACSCalibur and analysis was performed using FlowJo. Statistical analysis and graphical representation was performed using Excel and GraphPad Prism. The results are shown in FIG. 28. Briefly, treatment with K. pneumoniae antigenic compositions leads to an increase in both myeloid cells (likely monocytes and macrophages) as well as CD11b+ NK cells in the lungs of mice so treated.

With a focus of obtaining information with regard to cytokines being produced within lung tissue, the following experiments were conducted. Mice were either inoculated with 3×10⁵ Lewis Lung carcinoma cells or were injected with HBSS as a vehicle control. For mice inoculated with Lewis Lung carcinoma cells, they were pooled into a single cage where they were subsequently transferred at random to their respective cages. Thereafter, mice were treated with either K. pneumoniae antigenic compositions, or PBS, on days 2, 4, 6 and 8. Thereafter, all mice were sacrificed on day 9. To obtain information re: cytokine within lung tissue, a bronchoalveolar lavage was performed on the lungs. Thereafter, the lungs were surgically removed immediately after the lavage and placed into pre-weighed vials containing PBS and protease inhibitors. Thereafter, the lung tissue was homogenized, centrifuged, and the supernatant was applied to ELISA kits (eBioscience); the ELISA assay was carried out according to manufacturer's guidelines. Statistical analysis and graphical representation was performed using Excel and GraphPad Prism. Data is represented as pg of cytokine per mg of original lung tissue. Each data point in FIG. 29 is the value from a single mouse. As shown in FIG. 29, treatment with K. pneumoniae antigenic compositions leads to an increase in anti-tumour (IL-12, MCP-1, GMCSF, IL-6) cytokine production in the lung tissue.

With a focus of obtaining information with regard to cytokine production in the bronchoalveolar lavage (BAL) fluid, the following experiments were conducted. Mice were either inoculated with 3×10⁵ Lewis Lung carcinoma cells or were injected with HBSS as a vehicle control. For mice inoculated with Lewis Lung carcinoma cells, they were pooled into a single cage where they were subsequently transferred at random to their respective cages. Thereafter, mice were treated with either K. pneumoniae antigenic compositions, or PBS, on days 2, 4, 6 and 8 of the experiment. Thereafter, all mice were sacrificed on day 9. To obtain information with regard to cytokine production in the lungs, bronchoalveolar lavage was performed on the lungs of the mice. The fluid from the lavage was placed into vials, and stored at −80° C. until a time when ELISA assay was performed. Thereafter, the ELISA assay was carried out according to manufacturer's guidelines. Statistical analysis and graphical representation was performed using Excel and GraphPad Prism. Data is represented as pg/ml of lavage fluid as shown in FIG. 30. Each data point represents the value obtained from one mouse. As shown in FIG. 30, treatment with K. pneumoniae antigenic compositions had no effect on cytokine production in the BAL fluid.

With a focus on examining the M1/M2 macrophage phenotypes in the model described herein, NOS2 and Arg1 levels were monitored in the lung. The experiments conducted were as follows: briefly, mice were either inoculated with 3×10⁵ Lewis Lung carcinoma cells or were injected with HBSS as a vehicle control. For mice inoculated with Lewis Lung carcinoma cells, they were pooled into a single cage where they were subsequently transferred at random to their respective cages. Thereafter, mice were treated with either K. pneumoniae antigenic compositions, or PBS, on days 2, 4, 6 and 8 of the experiment. Thereafter, all mice were sacrificed on day 9. To obtain information with respect to NOS2 and Arg1 gene expression, 20 mice (5 from each group) had their lungs surgically removed. Thereafter, a small portion of these lungs were cut using sterile techniques and placed into RNA later to stabilize the RNA material for future gene analysis. Total RNA was extracted from the lung tissue using a kit from Qiagen and used according to manufacturer's protocol. A cDNA kit was used to convert an amount of RNA into cDNA (Qiagen), again by following instructions supplied by manufacturer. qPCR was conducted using primers designed to specifically amplify Nos2 and Arg1(Nos2: forward—CGCTTTGCCACGGACGAGA; reverse—AGGAAGGCAGCGGGCACAT; Arg1:forward—GGTCCACCCTGACCTATGTG; reverse—GCAAGCCAATGTACACGATG). Statistical analysis was conducted using Excel and GraphPad Prism. As shown in FIG. 31, treatment with K. pneumoniae antigenic compositions leads to an increase in the Nos2/Arg1 ratio in the lungs, which correlates with an enhanced anti-tumour response.

With a focus on investigating the M1/M2 response in the in vivo model described herein, the expression of CD206 (mannose receptor) was monitored. Briefly, mice were either inoculated with 3×10⁵ Lewis Lung carcinoma cells or were injected with HBSS as a vehicle control. For mice inoculated with Lewis Lung carcinoma cells, they were pooled into a single cage where they were subsequently transferred at random to their respective cages. Thereafter, mice were treated with either K. pneumoniae antigenic compositions, or PBS, on days 2, 4, 6 and 8 of the experiment. Thereafter, all mice were sacrificed on day 9. To obtain information with regard to CD206 expression, 20 mice (5 from each group) had their lungs surgically removed, and digested using Liberase TL and DNAse. Following the digesting and cell preparation, a single cell suspension was generated. A portion of the cells were transferred into 96 round bottom plates for staining using CD206 specific antibodies (clone MR5D3), acquired from Cedarlane Labs (Burlington, ON). As CD206 is located both intra- and extracellularly, the cells were first fixed using paraformaldehyde, and staining with the antibody in permeabilization solution. Analysis was performed using FlowJo. Statistical analysis and graphical representation was performed using Excel and GraphPad Prism. The results are shown in FIG. 32. As shown in FIG. 32, treatment with K. pneumoniae antigenic compositions leads to a reduction in CD206 expression on lung macrophages both in the presence (PBS+LL2 and K. pneumoniae 1/10X+LL2) or absence of lung tumours (PBS and K. pneumoniae 1/10X). In the presence of lung cancer, K. pneumoniae antigenic compositions reduce the frequency of CD206 expression from about 20% (PBS+LL2 group) to about 10% (K. pneumoniae 1110X+LL2 group). A similar reduction in CD206 expression was seen in K. pneumoniae treated animals without any lung cancer (PBS and K. pneumoniae 1110×).

With a focus on investigating the M1/M2 phenotypes in the in vivo model described herein, the expression of F4/80+ macrophages was monitored. Briefly, mice were either inoculated with 3×10⁵ Lewis Lung carcinoma cells or were injected with HBSS as a vehicle control. For mice inoculated with Lewis Lung carcinoma cells, they were pooled into a single cage where they were subsequently transferred at random to their respective cages. Thereafter, mice were treated with either K. pneumoniae antigenic compositions, or PBS, on days 2, 4, 6 and 8 of the experiment. Thereafter, all mice were sacrificed on day 9. To obtain information with respect to F4/80+ expression in macrophages, 20 mice (5 from each group) had their lungs surgically removed, and digested using Liberase TL and DNAse. Following digesting and cell preparation, a single cell suspension was generated. A portion of the cells were transferred into 96 round bottom plates for staining using F4/80 monoclonal antibodies. Cell data acquisition was performed using BD FACSCalibur. Analysis was performed using FlowJo. Statistical analysis and graphical representation was performed using Excel and GraphPad Prism. As shown in FIG. 33, treatment with K. pneumoniae antigenic compositions leads to a reduction in F4/80+ macrophages in the lungs. This reduction is thought to correlate with a reduction in M2-like macrophages.

Example 10 Site Specificity Studies (MOA14 Study)

With a focus on investigating the M1/M2 phenotypes in the in vivo model described herein which is used in conjunction with the antigenic compositions described herein, the following experiments were performed. Briefly, 5 mice per group were treated on day 0, 2, 4, and 6 with either PBS, E. coli colon antigenic compositions, or K. pneumoniae antigenic compositions. On day 7 of the experiment, the mice were sacrificed and a bronchoalveolar lavage was performed. Subsequently the lungs and proximal colon were removed and enzymatically digested. After digestion, the recovered cells were washed and stained with antibodies specific for I-A/I-E FITC (MHC class II; M5/114.15.2); anti-Gr-1 PE (RB6-8C5_; anti-CD11b PerCP-Cy5 (M1/70); anti-CD11c APC (N418). All antibodies were acquired from eBioscience (San Diego, Calif.). The lung cells were counted to determine the total number of cells (the colon was not counted because we did not remove equal amounts of colon between samples). After staining for 20 mins the cells were washed and analyzed by FACS. Each data point shown in corresponding FIG. 34 represents the frequency of CD11b+ Gr-1+ cells in the live gate for one mouse. As shown in FIG. 34, treatment with E. coli antigenic compositions leads to an increased frequency of inflammatory monocytes in the colon of treated mice.

Further, and as shown in FIG. 35, when monocytes in the lungs were examined based on the experimental methods detailed herein, it was found that while both E. coli and K. pneumoniae antigenic compositions increase the frequency of monocytes in the lungs of mice, K. pneumoniae antigenic compositions were more effective when counting for total numbers. Referring to FIG. 35, the left-most panel shows the frequency of CD11b+ Gr-1+ (inflammatory monocyte) cells in the lungs; the right-most panel shows the total number of CD11b+ Gr-1+ cells in the lung.

In an effort to examine the phenotype of macrophages present in tumours using the in vivo model described herein which is used in conjunction with the antigenic compositions described herein, M1-like and M2-like macrophages were examines. As shown in FIG. 36, this Figure represents the frequency of M1-like (see left panel of FIG. 36) TAMs (tissue associated macrophages) or M2-like (see right panel of FIG. 36) in subQ 4T1 tumours on day 8 post tumour implantation. As detailed herein, M1-like macrophages were defined as being CD11b+/Gr-1-/MHC Class II high; M2-like macrophages were defined as being CD11b+/Gr-1-/MHC Class II low.

Example 11 Indomethacin Efficacy and Anti-Inflammatory Studies

In an effort to examine the efficacy of combining antigenic composition treatment with indomethacin. Briefly, experiments were designed wherein there were 10 or 11 mice in each of 4 groups with all treatments beginning on day 4 after tumour inoculation. All mice received 50,000 4T1 mammary carcinoma cells subQ on day 0. Thereafter, the 4 groups were treated as follows: 1) Indomethacin daily (in drinking water)+PBS subQ every 2 days; 2) Indomethacin daily (in drinking water)+S. aureus antigenic composition subQ every 2 days; 3) Control vehicle daily (in drinking water)+PBS subQ every 2 days; and 4) Control vehicle daily (in drinking water)+S. aureus antigen composition subQ every 2 days. With respect to FIG. 37, the left-most panel of the Figure demonstrates the tumour volume for the various groups on day 15 of the experiment. The right-most panel demonstrates the frequency and makeup of the CD11b+ cells in the tumors on day 11 of the experiment. The frequency of CD11b+ cells is significantly increased in both of the Indomethacin treated groups relative to the control. These results demonstrate the efficacy of combining Staph. aureus antigenic compositions with anti-inflammatories, such as indomethacin. Further, and as shown in FIG. 38 herein, at the day 22 time point, indomethacin treatment resulted in an increase in CD11b+ cells.

To further examine the efficacy of combining antigenic composition treatment with indomethacin, a study was designed. Briefly, four (4) groups of 10-11 Balb/c mice per group received 10,000 4T1 carcinoma calls SQ on day 0. Thereafter, treatments were as follows: the first group received indomethacin (14 μg/ml in water) starting on day 4+PBS on days 4, 6, 8 etc.; the second group received indomethacin (14 μg/ml in water) and S. aureus antigenic compositions [0.1 ml of 0.5 OD 600 nm stock] starting on day 4+PBS on days 4, 6, 8 etc.; the third group received PBS starting on days 4, 6, 8 etc.; and the fourth group received S. aureus antigenic compositions [0.1 ml of 0.5 OD 600 nm stock] on days 4, 6, 8 etc. Tumor volume measurements were made on days 15, 19, and 22 and this data appears in FIG. 39 for the four (4) groups of mice. The data depicted in FIG. 39 sows that there is synergy between antigenic composition treatment and an anti-inflammatory (e.g., Indomethacin) in a subcutaneous cancel model.

On day 11 of the Experiment detailed above, tumors were excised and digested. Thereafter. The digested tumors were stained with anti-CD11b and analyzed by FACS (n=3 per group of mice). The results are depicted in FIG. 40 herein and demonstrate that there is an increased frequency of CD11b+ cells in the tumors of indomethacin treated mice at day 11 post-inoculation.

On day 22 of the Experiment detailed above, tumors were excised and digested. Thereafter. The digested tumors were stained with anti-CD11b and analyzed by FACS (n=7-8 per group of mice). The results are depicted in FIG. 41 herein and demonstrate that there is an increased frequency of CD11b+ cells in the tumors of indomethacin treated mice at day 22 post-inoculation. Further, FIG. 42 demonstrates that indomethacin treatment causes an increase in CD11b+ CD94+ myeloid cells in the tumors as found at day 22 post-inoculation.

To further examine whether the antigenic composition treatment was associated with an anti-inflammatory response, at day 22 of the Experiment described above, whole tumor samples were subjected to quantitative PCR by known methods. The gene products Fizz1 and Ym1 were targeted. Both Fizz1 and Ym1 are reportedly associated with M2 macrophages (see, for e.g., Wong et al. (2010) Eur. J. Immunol. 40(8): 2296-307). The results are depicted in FIG. 43 herein. As shown in FIG. 43, the relative expression of both Fizz1 and Ym1 was increased in tumors where there was treatment of both indomethacin and antigenic compositions (compared, for example, to indomethacin alone).

The relative expression levels of Arg1 and Fizz1 was examined in both the tumors and spleens of mice at day 22 of the Experiment. As shown in FIG. 44, both Arg1 and Fizz1 expression increased in the spleens of mice treated with indomethacin and antigenic compositions. The relative expression levels of Nos2 and Ym1 was examined in both the tumors and spleens of mice at day 22 of the Experiment. The relative expression levels are depicted in FIG. 45 herein for the four (4) groups of mice.

To further examine the anti-inflammatory response associated with the antigenic composition treatment, an experiment was designed as follows. Briefly, mice were given Lewis Lung tumors on day 0 [PBS and K. pneumoniae antigenic composition] or no tumors [PBS (no tumor)] or K. pneumoniae antigenic composition (no tumor)]. The mice received K. pneumoniae antigenic composition [0.1 ml of 0.5 OD500 nm stock] or PBS on day 2, 4, 6, 8. The mice were sacrificed on day 9 and their lungs were removed and homogenized. IFNγ was measured in the lung homogenate using ELISA. The results are shown in FIG. 46 herein. Treatment with K. pneumoniae antigenic composition reduced IFNγ production in the lungs of mice with and without lung tumors.

To further examine the anti-inflammatory response associated with antigenic composition treatment, the following experiment was designed. Briefly, bone marrow macrophages were cultured overnight either in media, or in medial supplanted with LPS, or in media supplanted with K. pneumoniae antigenic compositions. The media was tested for IL-12 and IL-10. The results are shown in FIG. 47 herein and demonstrate that IL-12 was not identified. As shown in FIG. 47, bone marrow macrophages cultured overnight with K. pneumoniae antigenic compositions produced IL-10. IL-10 is known to be associated with an anti-inflammatory response (see, for e.g., Bazzoni et al. (2010) Eur. J. Immunol. 40(9): 2360-8).

To further examine the anti-inflammatory response associated with antigenic composition treatment, the following experiment was designed. Briefly, the 4T1 tumor model was utilized to determine the effects of Staph aureus (SA) antigenic composition therapy to work synergistically with the anti-inflammatory drug indomethacin. In this study, there were four (4) groups of 10 Balb/c female mice which all received 50,000 4T1 mammary carcinoma cells subcutaneously on day 0. Group 1 received PBS subcutaneously every 2 days starting on day 4. Group 2 received SA [0.1 ml of 0.5 OD 600 nm] subcutaneously every 2 days starting at day 4. Group 3 and 4 received 14 ug/ml of indomethacin (indo) in their drinking water and subcutaneously received PBS and SA respectively every 2 days beginning on day 4. On day 22 the mice were sacrificed and tumors from 7-8 mice per group were harvested and placed in an RNA preserving agent. Subsequently we analyzed the expression of IL-10 in the tumors by real-time PCR. The results in FIG. 48 show that mice treated with indomethacin and PBS have a significant increase in IL-10 expression in the tumors. Treatment with indomethacin and SA leads to an even greater amount of IL-10 suggesting that SA enhances the anti-inflammatory effects of indomethacin in this tumor model. Since IL-10 is widely known to be an anti-inflammatory cytokine these results demonstrates that SA works synergistically with indomethacin in an anti-inflammatory manner. It is important to note that the tumors in the PBS group were the largest followed by the SA group and the Indo-PBS group. The tumors in the Indo-SA group were the smallest on day 22.

The anti-inflammatory properties of formulations of the invention can be employed for use in the treatment of a variety of inflammatory diseases, using endogenous pathogens or exogenous pathogens that are pathogenic in the tissue or organ within which the inflammation is situated, including bacterial, viral and fungal pathogens. Table 20 lists diseases characterized by inflammation (inflammatory conditions) which may be treated in accordance with alternative aspects of the invention.

TABLE 20 List of Chronic Inflammatory Diseases Acne vulgaris Acute disseminated encephalomyelitis Acute hemorrhagicleukoencephalitis Addison's Disease Agammaglobulinemia Allergies Alopecia areata Alzheimer's Amyotrophic Lateral Sclerosis Anaemia, autoimmune hemolytic Anaemia, pernicious Ankylosing spondylitis Anti-GBM/TBM Nephritis Antiphospholipid syndrome Antisynthetase syndrome Arteritis, temporal (also known as “giant cell arteritis”) Arthritis, juvenile Arthritis, psoriatic Arthritis, reactive (Reiter's syndrome, rea) Arthritis, rheumatoid Asthma Atherosclerosis Atopic allergy Atopic dermatitis Autoimmune enteropathy Autoimmune aplastic anemia Balo disease/Balo concentric sclerosis Bartter syndrome Bechets Syndrome Berger's disease Bickerstaff's encephalitis Blau syndrome Bronchitis, chronic Bullous pemphigoid Bursitis Cardiomyopathy, autoimmune Castleman's disease Celiac disease Celiac disease Chronic fatigue syndrome Chronic inflammatory demyelinating polyneuropathy Chronic recurrent multifocal osteomyelitis Churg-Strauss syndrome Cicatricialpemphigoid Cirrhosis, primary biliary Cogan syndrome Cold agglutinin disease Colitis Complement component 2 deficiency Connective tissue disease, mixed Connective tissue disease, undifferentiated COPD (chronic obstructive lung disease) Cranial arteritis CREST syndrome Cryoglobulinemia Cushing's Syndrome Cutaneous leukocytoclasticangiitis Cystitis, interstitial Dacryadenitis Dego's disease Dercum's disease Dermatitis Dermatitis herpetiformis Dermatitis, autoimmune progesterone Dermatomyositis Diabetes Diabetes insipidus, nephrogenic Diabetes mellitus type 1 Diffuse cutaneous systemic sclerosis Discoid lupus erythematosus Diverticulitis Dressler's syndrome Dysmenorrhea (menstrual cramps/pain) Eczema Eczema Endometriosis Enthesitis-related arthritis Eosinophilic fasciitis Eosinophilic gastroenteritis Epidermolysisbullosaacquisita Erythema nodosum Essential mixed cryoglobulinemia Evan's syndrome Fibrodysplasiaossificansprogressiva Fibromyalgia Fibrosingaveolitis Gastritis, atrophic Gastritis, atrophic Gastrointestinal pemphigoid Giant cell arteritis Glomerulonephritis Glomerulonephritis Goodpasture's syndrome Gout, acute Gout, arthritic Graves' disease Guillain-Barré syndrome (GBS) Haemolytic anaemia Hashimoto's encephalitis Hashimoto's thyroiditis Hemolyticanemia, autoimmune Henoch-Schonleinpurpura Hepatitis, autoimmune Hepatitis, viral Herpes gestationis Hypogammaglobulinemia Idiopathic Inflammatory Demyelinating Diseases Idiopathic pulmonary fibrosis Iga nephropathy Ileus (bowel obstruction) Inclusion body myositis Inflammatory bowel disease, Crohn's disease Inflammatory bowel disease, ulcerative colitis Inflammatory demyelinating polyneuopathy Inner ear disease, autoimmune Interstitial cystitis Irritable bowel syndrome (IBS) Juvenile idiopathic arthritis Juvenile rheumatoid arthritis Kawasaki's Disease Kidney stones Lambert-Eaton myasthenic syndrome Leukocytoclasticvasculitis Lichen planus Lichen sclerosus Linear iga disease (LAD) Lou Gehrig's disease (Also Amyotrophic lateral sclerosis) Lupoid hepatitis Lupus Lupus erythematous Lymphoproliferative syndrome, autoimmune Majeed syndrome Ménière's disease Meningitis Microscopic polyangiitis Miller-Fisher syndrome Morphea Mucha-Habermann disease Multiple sclerosis Multiple sclerosis Myasthenia gravis Myositis Myositis, inclusion body Nephritis Nephrotic syndrome Neuromyelitisoptica (Also Devic's Disease) Neuromyotonia Occularcicatricialpemphigoid Ocular inflammation (acute and chronic non-bacterial inflammation of the anterior part of the eyes) Opsoclonus myoclonus syndrome Ord thyroiditis Osteoarthritis Paget's disease of bone Palindromic rheumatism Pancreatitis, autoimmune PANDAS (pediatric autoimmune neuropsychiatric disorders associated with streptococcus) Paraneoplastic cerebellar degeneration Parkinson's Paroxysmal nocturnal hemoglobinuria (PNH) Parry Romberg syndrome Pars planitis Parsonnage-Turner syndrome Pelvic inflammatory disease Pemphigus Pemphigus vulgaris Pericarditis, non-rheumatic Peripheral neuropathy, autoimmune Perivenous encephalomyelitis POEMS syndrome Polyarteritisnodosa Polychondritis, relapsing Polyendocrine syndrome, autoimmune Polymyalgia rheumatica Polymyalgia rheumatica Polymyositis Primary sclerosing cholangitis Progressive inflammatory neuropathy Prostatitis, chronic Pseudogout Psoriasis Psoriasis Pure red cell aplasia Pyodermagangrenosum Rasmussen's encephalitis Raynaud phenomenon Reiter's syndrome Restless leg syndrome Retinopathy of prematurity Retroperitoneal fibrosis Rheumatoid fever Rhinitis, allergic Sarcoidosis Sarcoidosis Schmidt syndrome Schnitzler syndrome Scleritis Scleroderma Sclerosis, systemic Sjögren's syndrome Spondyloarthropathy Still's disease Subacute bacterial endocarditis (SBE) Susac's syndrome Sweet's syndrome Sydenham chorea Sympathetic ophthalmia Takayasu's arteritis Temporomandibular joint disorder (TMJD or TMD), or TMJ syndrome Thrombocytopenic purpura, autoimmune Thrombocytopenic purpura, idiopathic Tolosa-Hunt syndrome Transplant rejection Transverse myelitis Undifferentiated spondyloarthropathy Urticaria Uveitis, autoimmune Valvular disease, non-rheumatic Vasculitis Vitiligo Wegener's granulomatosis

As provided in Table 20 above, arthritis is a chronic inflammatory disease. In particular, arthritis is understood to be a description of inflammation of one or more joints. There are many types of arthritis, which include (but are not limited to) the following: Ankylosing spondylitis, Behcet's disease, Ehlers-Danlos Syndrome, Familial Mediterranean fever, Fibromyalgia, Fifth disease, Giant cell arteritis, Gout, Haemochromatosis, Henoch-Schönleinpurpura, Hyperimmunoglobulinemia D with recurrent fever, Inflammatory bowel disease arthritis (including Crohn's Disease and Ulcerative Colitis), Juvenile rheumatoid arthritis, Juvenile spondyloarthropathy, Lyme disease, Marfan syndrome, Osteoarthritis, Pseudo-gout, Psoriatic arthritis, Reactive Arthritis (Reiter's syndrome), Rheumatoid arthritis, Sarcoidosis, Scleroderma, SEA syndrome (seronegativity, enthesopathy, arthropathy), Sjogren's syndrome, Still's disease, Systemic lupus erythematosus (SLE), TNF receptor associated periodic syndrome, and Wegener's granulomatosis (and other vasculitis syndromes).

In alternative aspects of the invention, arthritis can be treated using formulations of the invention that include pathogens, such as bacteria, that infect joint regions. For example, the following bacteria/bacterial species, known to infect the joint regions, may be used in formulations of the invention for treating an arthritis: Staphyloccus aureus; Coagulase negative Staphylococci; Streptococcus pneumoniae; Streptococcus species; Pseudomonas aeruginosa; Mycobacterium tuberculosis; Neisseria meningitides; Mycobaterium bovis; Enterococcus species; Salmonella enteritidis; Escherichia coli; Proteus species; Serratia species; Acinetobacter species; Enterobacter species; Pasteurella species; Campylobacter species; Brucella species; Haemophilus influenza; Neisseria gonorrhoeae; Mycobacterium xenopi; Mycobacterium leprae; Coxiella burnetti; Bartonella species; Actinomadura Madura; Streptomyces somaliensis; Borrelia burgdorferi; and Yersinia species. Further, and for example, the following viral species are known to infect the joint regions: Enterovirus; Dengue virus; Hepatitis B; Hepatitis C; HIV; Human parovirus; Mumps virus and Rubella. Further, the following fungal species are known to infect the joint regions: Coccidioides immitis; Candida albicans; Blastomyces dermatitidis; Histoplasma capsulatum; Cryptococcus neoformans; Paracoccidioides brasiliensis; Sporothrix schenckii; and Penicillium marneffi. Further, and for example, the following helminth or protozoa species are known to infect the joint regions: Loa loa; Mansonella streptocerca; Onchocerca volvulus; Dracunculus medinersis; Gnathostoma spinigerum; Schistomsoma species; Strongyloides stercoralis; Echinococcus species; Trichinella spiralis; and Giardia species. The foregoing examples are representative, and are not limiting.

In alternative aspects, arthritis may be treated using preparations made with one or more endogenous pathogens: Staphyloccus aureus; Coagulase negative Staphylococci; Streptococcus pneumoniae; Streptococcus species; Pseudomonas aeruginosa; Enterococcus species; Salmonella enteritidis; Escherichia coli; Proteus species; Serratia species; Acinetobacter species; Enterobacter species; Pasteurella species; Campylobacter species; or Haemophilus influenza. Alternatively, the pathogen may be exogenous: Mycobacterium tuberculosis; Neisseria meningitides; Mycobaterium bovis; Brucella species; Neisseria gonorrhoeae; Mycobacterium xenopi; Mycobacterium leprae; Coxiella burnetti; Bartonella species; Actinomadura Madura; Streptomyces somaliensis; Borrelia burgdorferi; and Yersinia species. Alternatively, the pathogen may be a virus: Enterovirus; Dengue virus; Hepatitis B; Hepatitis C; HIV; Human parovirus; Mumps virus and Rubella. Alternatively, the pathogen may be a fungal species: occidioides immitis; Candida albicans; Blastomyces dermatitidisl; Histoplasma capsulatum; Cryptococcus neoformans; Paracoccidioides brasiliensis; Sporothrix schenckii; and Penicillium marneffi. Alternatively, the pathogen may be a helminth or protozoa species: Loa loa; Mansonella streptocerca; Onchocerca volvulus; Dracunculus medinersis; Gnathostoma spinigerum; Schistomsoma species; Strongyloides stercoralis; Echinococcus species; Trichinella spiralis; and Giardia species.

In further alternative embodiments, arthritis may be treated using preparations made with bacterial pathogens that are common causes of bone infection: Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus agalactiae, other streptococci spp., Escherichia coli, Pseudomonas spp., Enterobacter spp., Proteus spp., Serratia spp., Neisseria gonorrhea, Salmonella spp., Mycobacterium tuberculosis, Haemophilus influenza; or, common viral pathogens parvovirus B19, rubella, hepatitis B; or, a common fungal pathogen: Scedosporium prolificans.

Example 12 Inflammatory Bowel Disease Studies

This example provides an illustration of the clinically effective use of an antigenic formulation comprising killed E. coli in the treatment of a patient with Crohn's disease, over a three-month course of treatment. During the course of treatment, the patient became symptom free and ceased using anti-inflammatory medications.

The patient initially presented reporting pain in the area of the large intestine and diarrhea, while under treatment with prednisone and Imuran™.

Treatment was initiated with a subcutaneous inoculum of a killed formulation of whole E. coli, derived from an E. coli strain collected from a patient with an E. coli colonic infection. The dosing schedule involved a subcutaneous dose every second day, beginning with a 0.05 ml dose, gradually increasing in volume until a 2 inch diameter light pink/red skin response was achieved within 24 hours after injection at the injection site. The dose eventually required to achieve this skin response was 0.09-0.11 ml in this patient, and this dose has been continued as a maintenance dose every second day.

One week following the initiation of treatment with the antigenic preparation of whole killed E. coli, the patient reported that the pain and diarrhea were gone. Within about two months, the patient discontinued treatment with prednisone while continuing on a daily does of 150 mg of Imuran™ Subsequently, the patient also discontinued use of Imuran™

By two-months following the initiation of treatment with the E. coli composition, the patient was self-administering 0.09-0.11 ml of the E. coli preparation every other day. The patient self-adjusted this dosage so as to provoke a local inflammatory reaction evidenced by a pink spot of approximately 2 inches in diameter that persisted at the site of administration for about two days. This patient is also described in later studies detailed in Example 15 herein.

Example 13 Fungal Studies

Experiments utilizing the lung mouse model system described in detail herein were conducted which determined that mice that had received water contaminated with a particular fungal species (Penicillium marneffei), which is known to cause respiratory infections in both mice and humans, demonstrated decreased tumor burden as has been demonstrated and discussed with respect to bacterial lung pathogens.

Numerous fungal species are known to be associated with various organs or tissues as detailed in Table 21 below that water contaminated with fungal species also resulted. Accordingly, and based on the experimental principles detailed herein, the specificity demonstrated herein with respect to bacterial and viral pathogens should be extendable to fungal pathogens as well.

TABLE 21 Fungal species and associations with organs/tissues Duodenum Fungus Skin Respiratory Genital GU system Mouth Stomach Jejunum Ileum Colon Other Actinomadura X species Alternaria species X sinuses Aspergillus X sinuses, fumigatus brain Bipolaris species X sinuses Blastomyces X X X bones species Candida alibcans X X X X oesophagus Candida krusei Cladophialophora X sinuses carrionii Coccidiodes immitis X Coccidiodes posadasii Cryptococcus X neoformans Cryptococcus gattii Curvularia species X sinuses Epidermophyton X species Exophiala species X sinuses Fonsecaea pedrosoi X Fusarium species X X sinuses Histoplasma X capsulatum Microsporum X species Nocardia species X Paecilomyces X X sinuses species Paracoccidioides X X X brasiliensis Pityrosporum X species Penicillium marneffei X X systemic infection Pneumocystis X jiroveci Pseudallescheria X X sinuses boydii (Scedosporium apiospermum) Rhizopus species X X X X X sinuses, (Rhizo)Mucor orbits, brain, species Absidia species Cunninghamella species Scedosporium X X sinuses prolificans Sporothrix schenckii X Stachybotrys X chartarum Tinea capitis X Tinea cruris Tinea pedis Trichoderma X X sinuses longibrachiatium Trichophyton X species Trichosporon X X sinuses species

Example 14 Arthritis Studies

Patient BA. Patient BA was diagnosed at age 18 with Crohn's disease. In addition to gastrointestinal symptoms associated with Crohn's disease, she also had Crohn's arthritis symptoms (join aches and stiffness), the most common extraintestinal manifestation of Crohn's disease. She was treated with prednisone, Remicade™ and other medications, but continued to have symptoms in spite of this treatment. At the age of 33, the patient was continuing to have ongoing symptoms of abdominal pain and diarrhea and joint pain and stiffness in spite of treatment with long-term prednisone. Her joint symptoms were severe. She described her joint symptoms and their impact on her life as feeling like a “frozen snowman” due to the joint pain and stiffness. On Aug. 22, 2011, the patient started treatment with antigenic compositions derived from E. coli. More specifically, treatment was initiated with a subcutaneous inoculum of a killed formulation of whole E. coli, derived from an E. coli strain collected from a patient with an E. coli colonic infection. Within 4 days of starting the E. coli treatment described herein, her gastrointestinal symptoms resolved completely and remained in remission with E. coli treatment.

However, her joint symptoms (not targeted by E. coli antigenic compositions) continued unabated. She was still having severe joint pain (shoulders, hands, neck, low back, knee) and joint stiffness in spite of treatment with 20 mg prednisone daily and ibuprofen. On Sep. 25, 2011, Patient BA began treatment with antigenic compositions derived from S. aureus, given every second day by s.c. injection, to target her arthritis symptoms (S. aureus is the most common cause of bone and joint infection). More specifically, treatment was initiated with a subcutaneous inoculum of a killed formation of whole S. aureus, derived from a S. aureus strain collected from a patient with a S. aureus abscess infection. She began treatment with a dose of 0.05 ml and gradually increased the dose until a 1-2 inch (diameter) light pink/red skin response was achieved 24 hours after the injection at a dose of 0.25 ml, which she then maintained every second day. After 10 days of treatment with antigenic compositions derived from S. aureus, her joint symptoms began to improve with decreased joint pain and symptoms and the patient began weaning off prednisone. Her joint symptoms continued to improve and she discontinued prednisone and no longer required ibuprofen for pain. After 2 months of treatment with S. aureus as described herein, this patient's joint symptoms had resolved completely. Three months after starting S. aureus treatment as described herein, the patient remains free of joint symptoms and fully active.

Patient BB. Patient BB had severe rheumatoid arthritis with severe bone deformity, joint pain and morning stiffness which was resistant to treatment with Plaquenil™, methotrexate, prednisone and other standard treatments. Rheumatoid factor 343 IU/ml (normal 0-20 IU/ml). At the time Patient BB began treatment with S. aureus, she was on treatment with long-term methotrexate, 20 mg prednisone and a non-steroidal anti-inflammatory agent (NSAID). Patient BB started on treatment with antigenic compositions derived from S. aureuson Nov. 14, 2011 by s.c. injection every second day. She gradually increased the dose of antigenic compositions derived from S. aureus from 0.05 ml to 0.10 ml until a 1 inch diameter skin response was achieved at the injection site 24 hours after s.c. injection. She has maintained this dose every second day, with a 1 inch skin response at the site of injection 24 hours after injection. By Dec. 6, 2011, 3 weeks after the treatment had begun as described herein, her symptoms had begun to improve significantly. By Dec. 20, 2011, after 5 weeks of treatment as described herein, Patient BB reported that joint symptoms had improved further and that her morning stiffness had “reduced tremendously”. She discontinued methotrexate treatment. She continued to improve and, by Jan. 6, 2011, after 7 weeks of treatment with antigenic compositions derived from S. aureus, her morning stiffness had resolved completely and her joint pain throughout the rest of the day had improved significantly (from a score of 6/10 to 3/10). This positive result with antigenic compositions derived from S. aureus treatment was particularly surprising to the patient since her disease symptoms had been previously resistant to other arthritis treatments.

Example 15 Crohn's Disease Studies

Patient AA. This patient was previously described at an earlier time point in Example 12. This example provides a further and continued illustration of the clinically effective use of an antigenic formulation comprising killed E. coli in the treatment of a patient with Crohn's disease, over an eleven-month course of treatment with complete sustained remission of disease. During the course of treatment, the patient became symptom free and ceased using anti-inflammatory medications. The patient was diagnosed with Crohn's disease in July 2006, with symptoms of bloody diarrhea and weight loss (30 pound weight loss). Colonoscopy revealed Crohn's disease in the cecum, ascending, transverse and descending colon. He began on treatment with Imuran™ and intermittent treatment with prednisone. In spite of these medications, his symptoms of abdominal pain and loosed stools persisted with flare ups of bloody diarrhea. In July 2010, his symptoms worsened in spite of treatment with Imuran and prednisone. He began treatment with antigenic compositions derived from E. coli on Jul. 26, 2010. Treatment was initiated with a subcutaneous inoculum of a killed formulation of whole E. coli, derived from an E. coli strain collected from a patient with an E. coli colonic infection. The dosing schedule involved a subcutaneous dose every second day, beginning with a 0.05 ml dose, gradually increasing in volume until a 2 inch diameter light pink/red skin response was achieved within 24 hours after injection at the injection site. The dose eventually required to achieve this skin response was 0.09-0.11 ml in this patient, and this dose was continued as a maintenance dose every second day. The patient self-adjusted the dosage so as to provoke a local inflammatory reaction evidenced by a pink spot of approximately 2 inches in diameter that persisted at the site of administration for about two days.

After 1 week of treatment with antigenic compositions derived from E. coli, the patient's symptoms of abdominal pain and diarrhea resolved completely and he was able to return to work. He began weaning off of prednisone and discontinued prednisone on September 15^(th). After 3 weeks of treatment as described herein, he had gained 14 pounds and was feeling in excellent health. On Sep. 28, 2010, a repeat colonoscopy showed no signs of Crohn's disease activity. On Oct. 18, 2010, the patient stopped Imuran treatment.

The patient remained completely symptom free and in excellent health, the first time he had felt well since his diagnosis of Crohn's disease 4 years before. While stress, travel, or alcohol had precipitated flare ups previously, the patient was now able to travel and eat or drink whatever he liked and he remained symptom free. He regained 26 pounds and was able to return to a full and active life.

On Jul. 1, 2011, after eleven months of treatment with antigenic compositions derived from E. coli, the patient remained symptom free and in excellent health and discontinued treatment on that date. Six months later, in January, 2012, the patient remains symptom free and in full sustained clinical remission from Crohn's disease.

Patient AB. Patient AB was diagnosed with Crohn's disease in November 2009 by colonoscopy, after having abdominal pains since July 2009. The patient initially declined treatment. However, her symptoms worsened substantially, with severe abdominal pain, bloody stool and 15 pound weight loss. She was hospitalized Jun. 25, 2011, at which time she was treated with i.v. fluids and antibiotics. She took two doses of prednisone but then discontinued prednisone treatment due to concerns with respect to potential side effects. On Jul. 27, 2011, she began treatment with antigenic compositions derived from E. coli by s.c. injection every second day, beginning with a dose of 0.05 ml and gradually increasing the dose till a 2 inch diameter light pink skin response was achieved at the site of injection 24 hours after injection at a dose of 0.10 ml. The 0.10 ml was then continued as the maintenance dose, with the resultant 2 inch skin response following each s.c. injection. During the period prior to the initiation of the treatment with antigenic compositions derived from E. coli, the patient was having cramping abdominal pain with bloating and loose stools. Within 3 days of starting the treatment as described herein, the patient's gastrointestinal symptoms resolved completely and the patient's bowel movements became well-formed and regular, the first time that she had regular bowel movements “in years”. Patient AB's symptoms remained in complete remission and she continued treatment with antigenic compositions derived from E. coli for 3 months. After 3 months of treatment, she discontinued treatment. Two months after stopping the treatment as described herein, the patient remains symptom free and in full clinical remission from Crohn's disease.

Patient AC. Patient AC was diagnosed with Crohn's disease in July 2007 by colonoscopy. She was treated with Asacol™, but was having cramping abdominal pains and 3-4 bowel movements per day in spite of this treatment. She would get “flare ups” with constant abdominal pain if she ate certain foods (e.g., high fibre foods, dairy). On Jul. 7, 2011, Patient AC began treatment with antigenic compositions derived from E. coli by s.c. injection every second day, with an initial dose of 0.05 ml gradually increasing till a 1-2 inch diameter pink skin response was achieved at the injection site 24 hours after injection at a dose of 0.1 ml, which she then maintained every second day. Within one week of starting the treatment as described herein, her gastrointestinal symptoms resolved completely and she began having normal once-daily bowel movements. She began eating foods that previously would have caused ‘flare ups’ and did not have any symptoms after consuming these foods. After 5 weeks of the treatment with antigenic compositions derived from E. coli, Patient AC discontinued Asacol treatment. Even though in the past when she missed an Asacol dose she would get a flare-up, she remained symptom free after stopping Asacol while on treatment with antigenic compositions derived from E. coli. After 3.5 months of treatment as described herein, Patient AC remained in complete clinical remission from Crohn's disease and discontinued SSI treatment on Oct. 25, 2011. Two months after stopping treatment with antigenic compositions derived from E. coli, the patient remains symptom free and in full clinical remission from Crohn's disease.

Patient AD. Patient AD was diagnosed with Crohn's disease in 1998 by colonoscopy. She was treated with various Crohn's disease treatments in the past, including prednisone, Purinethol™, Pentasa™, and Entocort EC™ without improvement of disease symptoms and therefore, she discontinued these treatments. Patient AD began treatment with antigenic compositions derived from E. coli on 29 Aug., 2011, at which time she was having cramping abdominal pains with diarrhea (3-5 loose bowel movements per day). Patient AD's Crohn's symptoms began to improve 2 weeks after initiation of the treatment. After 2.5 months of treatment, Patient AD was symptom free, with one normal firm bowel movement per day, the first time she had had normal regular bowel movements since her diagnosis with Crohn's disease 13 years previously. 4 months after starting the treatment with antigenic compositions derived from E. coli, Patient AD remains on treatment with antigenic compositions derived from E. coli and in full clinical remission from Crohn's disease.

Patient AE. Patient AE was diagnosed at age 18 with Crohn's disease. She was treated with prednisone, Remicade™ and other medications, but continued to have symptoms in spite of these treatments, and therefore, had discontinued all other treatments except prednisone. At the age of 33, the patient was continuing to have ongoing symptoms of abdominal pain and diarrhea in spite of treatment with long-term prednisone. On Aug. 22, 2011, the patient started treatment with antigenic compositions derived from E. coli, with an initial dose of 0.05 ml s.c., gradually increased till a 1-2 inch pink skin response occurred 24 hours after injection, at a dose of 0.08 ml, which the patient then maintained every second day. Within 4 days of starting the treatment as described herein, the patients gastrointestinal symptoms resolved completely, which the patient described as “very surprising and fantastic” considering that she had been on many other Crohn's medications in the past without resolution of her symptoms. The patient weaned off prednisone treatment and remained symptom free on treatment with antigenic compositions derived from E. coli. Four months after starting the treatment, the patient remains free of Crohn's gastrointestinal symptoms and in full clinical remission on the treatment.

Patient AF was diagnosed with severe Crohn's disease in 1995, with disease throughout his small and large intestine. He had been treated with many different Crohn's disease medications, including Remincade™, Asacol™ prednisone and many other treatments and experimental therapies, without success in controlling his disease. He had had multiple surgeries and hospitalizations. Prior to the initiation of treatment with antigenic compositions derived from E. coli, he had been on daily prednisone (20 mg per day) for 7 years. Patient AF began treatment with antigenic compositions derived from E. coli on Sep. 16, 2011. At that time, he was having constant cramping abdominal pain with 20 loose/watery bowel movements per day. He began with a dose (of antigenic compositions of E. coli) of 0.05 ml and gradually increased the dose until a 1 inch diameter skin response was achieved 24 hours after s.c. injection at a dose of 0.15 ml, which he has continued as a s.c. maintenance dose every second day. Within 1 week of starting treatment with antigenic compositions derived from E. coli, his symptoms of abdominal cramping resolved. After 1 month of the treatment, his bowel movements became firmer and bowel movement frequency has reduced from 20 bowel movements per day to 5-10 bowel movements per day. After 4 weeks of the treatment as described herein, Patient AF began reducing the dose of prednisone. In the past, reducing the dose of prednisone resulted in worsening of Crohn's symptoms. While on treatment with antigenic compositions derived from E. coli, reducing prednisone dose did not result in worsening of symptoms. After 3.5 months of the treatment, patient AF has reduced his dose of prednisone to 5 mg per day (from 20 mg per day prior to the start of the treatment), has remained free of abdominal pain for 3 months and has substantially less bowel movements per day (5-10 vs. 20) than when he began treatment with antigenic compositions derived from E. coli, indicating that, while not in remission, his Crohn's disease and clinical symptoms have substantially improved on the treatment with antigenic compositions derived from E. coli.

Example 16 Mouse Colitis Studies Disease Studies

A DSS-induced colitis model was developed (see, for e.g., Pizarro et al. (2003) TRENDS in Molecular Medicine 9(5)). Briefly, groups of 5 female C57BL/6 mice were given 3% DSS in their drinking water from Day 0-7. Either antigenic compositions derived from E. coli or PBS were administered 0.05 ml subcutaneously every 2 days starting on day 0. The weight of the animals was monitored daily for 7 days and data in FIG. 49 herein represents the average weight change of the mice over the course of treatment. Mice treated with antigenic compositions derived from E. coli lost less weight.

On day 7 of the experiment, the mice were sacrificed and their colons were removed and homogenized. As shown in FIG. 50 herein, IL-17 levels in E. coli treated mice are reduced compared to PBS treated control mice in the colon 7 days after the start of DSS treatment. IL-17AF levels were measured in the homogenized colon samples using a bead array.

Further, in a related study the efficacy of treating dextran sulphate sodium(DSS)-induced murine colitis with antigenic compositions derived from E. coli was illustrated. Colitis was induced in BALB/c mice by 3.5% DSS dissolved in the drinking water for 10 days. Placebo or antigenic compositions derived from E. coli (0.03 mL of undiluted SSI) was administered subcutaneously every other day beginning on the first day of 3.5% DSS exposure. To assess in vivo efficacy, a clinical disease activity score was evaluated daily. Specifically, the body weight, occult blood or the presence of gross blood per rectum, and stool consistency were determined daily as described previously (Dieleman et al., 1997; Hartmann et al., 2000; Siegmund et al., 2001). The score was derived as follows: weight loss<1% counted as 0 points, weight loss of 1 to <5% as 1 point, 5 to <10% as 2 points, 10 to 20% as 3 points, and more than 20% as 4 points. For stool consistency, 0 points were given for well formed pellets; 2 points for pasty and semi-formed stools, which did not stick to the anus, and 4 points for liquid stools that did stick to the anus. Bleeding was scored 0 points for no blood in hemoccult; 2 points for positive hemoccult; and 4 points for gross bleeding. The average of these three scores (body weight, stool consistency, and rectal bleed) gave an overall clinical score. The data is represented in FIG. 51 herein. The results of this study demonstrate a trend towards a decrease in colitis disease clinical score when mice received antigenic compositions derived from E. coli with day 10 reaching significance (p-value=0.0442 using unpaired, two-tailed T-test), relative to PBS.

Further, in a related study, the effect of treatment with antigenic compositions derived from E. coli was investigated to determine its efficacy in dextran sulphate sodium (DSS)-induced murine colitis. Colitis was induced in 10 C57BL/6 mice by giving 3% DSS dissolved in the drinking water for 7 days prior to placebo or E. coli antigenic composition treatment. Water containing DSS was replaced with regular drinking water and placebo or antigenic compositions derived from E. coli (0.05 mL of undiluted SSI) was administered subcutaneously every other day beginning on day 7 post 3% DSS exposure. To assess in vivo efficacy, protection from weight loss due to DSS-induced colitis, the body weight was measured daily. There were 5 mice per treatment group. The average percent weights of the mice in their respective groups were plotted.

The results of this study demonstrate a decrease in colitis disease as measured by protection from weight loss when mice, which had colitis induced with DSS from days 1 to 6, received treatment with antigenic compositions derived from E. coli from days 7 to 15, which reached statistical significance (p-value<0.04 using unpaired, two-tailed T-test), relative to PBS. Treatment of mice with antigenic compositions derived from E. coli has a therapeutic benefit after colitis was induced. The results are depicted in FIG. 52.

Example 17 Personalized Site-Specific Immunomodulation Studies

The clinical and preclinical data on the site-specificity of killed bacterial preparations for the treatment of cancer and chronic inflammation provide support for the view that the host immune system is able to recognize the bacteria and mount an immune response where that bacterium is likely to cause an infection. Accordingly, we tested whether a previous exposure to a bacterial species determines whether an antigenic composition comprised of components of that bacterial species can induce a site-specific immune response.

In order to test this hypothesis, a study was conducted where we have measured the therapeutic efficacy of S. pneumoniae antigenic compositions for the treatment of lung cancer in mice that have either never been exposed to S. pneumoniae (note: not a natural lung pathogen in mice), are currently colonized by S. pneumoniae, or were previously exposed to S. pneumoniae but have cleared the colonization before the start of the study (see: Experimental Setup in Table 22).

TABLE 22 Experimental Setup for Personalized Site-Specific Immunomodulation Studies Day −21 Day−3 Day 0 1 2 3 4 5 6 7 8 9 10 21 Is SSI treatment more/less/equally effective in mice that have previously been or are currently colonized with S. pneumoniae? Group 1A Colonize LLC SSI SSI SSI SSI SSI Terminate experiment with strain P1121 Group 1B saline LLC SSI SSI SSI SSI SSI Terminate experiment (no mice expected to survive in this group) Group 1C LLC Terminate experiment Group 1D Colonize LLC SSI SSI SSI SSI SSI Terminate experiment with strain P1121 1st collection 2nd collection In the first and second collections 5mice per group will be sacrificed and lung flow (MDSC, T cells, NK myeloid cells assessed), cytokines (lung & serum), histology performed, tumour nodules counted etc At least 10 mice will be in each group for survival studies.

For these studies, mice were challenged intranasally with a strain of S. pneumoniae (P1121) which normally colonizes the nasal cavity of humans and which can cause acute colonization in mice (see, for e.g. McCool and Weiser (2004), Limited role of antibody in clearance of Streptococcus pneumoniae in a murine model of colonization. Infect Immun., 72(10): p. 5807-13; and van Rossum et al. (2005) Host and bacterial factors contributing to the clearance of colonization by Streptococcus pneumoniae in a murine model. Infect Immun., 73(11): p. 7718-26). Two groups of mice received no S. pneumoniae challenge, 1 group received S. pneumoniae on Day −28 (past exposure), and the last group received S. pneumoniae on Day −3 (current exposure) (see: Table 22). On Day 0 all mice received Lewis Lung Carcinoma (LLC) cells intravenously. Starting on Day 2, three of the four groups started receiving subcutaneous treatment with S. pneumoniae antigenic composition which was continued every two days until death. Mice which had never been exposed to S. pneumoniae showed no survival benefit when treated with S. pneumoniae antigenic composition. This was expected based on the fact that S. pneumoniae is not a natural lung pathogen in mice. Strikingly however, lung cancer-bearing mice that were either currently colonized or had previously cleared pulmonary S. pneumoniae colonization survived significantly longer when treated with S. pneumoniae antigenic composition (see FIG. 53). These results indicate that previous exposure to a particular bacterial species is a predetermining factor of the efficacy of an antigenic composition generated from that bacterial species. Accordingly, personalized site-specific immunomodulation can be developed for a subject based on a subject's prior exposure to a particular pathogen species, such as a bacterial pathogen as detailed herein. Personalized site-specific modulation based on prior exposure to a pathogen is not limit to bacterial pathogens; rather, as detailed herein, it is specifically contemplated that prior exposure to viral pathogens, fungal pathogens, protozoan pathogens, and helminth pathogens would elicit the same immunological response.

Accordingly, In one aspect, a method of treating an individual for a condition characterized by inflammation in a specific organ or tissue. The method involves determining whether the individual has previously been infected with at least one pathogen that is pathogenic in the specific organ or tissue; and administering to the individual an anti-inflammatory composition comprising antigenic determinants, the antigenic determinants selected or formulated so that together they are specific for the at least one pathogen.

In another aspect, a method of formulating an anti-inflammatory composition for treating an individual for a condition characterized by inflammation in a specific organ or tissue. The method involves determining whether the individual has previously been infected with at least one pathogen that is pathogenic in the specific organ or tissue; producing an antigenic composition comprising antigenic determinants that together are specific for the at least one pathogen; and formulating the antigenic composition for administration as an anti-inflammatory composition capable of eliciting an anti-inflammatory response in the specific organ or tissue.

The methods detailed herein may involve identifying the presence of at least one antibody that recognizes the at least one pathogen. The methods may involve identifying at least one memory B cell that recognizes the at least one pathogen. The methods may involve identifying at least one memory T cell that recognizes the at least one pathogen. The methods may involve the at least one antibody, the at least one memory B cell, or the at least one memory T cell being obtained from peripheral circulation of the individual.

In another aspect, a method of treating an individual for a condition characterized by inflammation in a specific organ or tissue. The method involves administering to the individual an infectious dose of at least one pathogen that is pathogenic in the specific organ or tissue; and administering to the individual an anti-inflammatory composition comprising antigenic determinants, the antigenic determinants selected or formulated so that together they are specific for the at least one pathogen. The method may involve these two administration steps occurring simultaneously. The method may involve the second step occurring between 1 hour and 30 days after the first step.

As used herein the term “infectious dose” means a dose that is sufficient to result in infection in a specific organ or tissue without resulting in systemic infection in the individual.

The methods detailed herein may involve a timour being situtated in the specific organ or tissue of the individual.

The methods detailed herein may involve the anti-inflammatory composition being formulated for subcutaneous injection or intradermal injection. Further, the anti-inflammatory composition may be formulated for repeated subcutaneous or intradermal injection. Further, the anti-inflammatory composition may be formulated for injection to produce a localized skin immune response at a site of administration.

Further, the methods detailed herein may involve the at least one pathogen being endogenous to the specific organ or tissue. Further, the methods detailed herein may involve the at least one pathogen being exogenous to the specific organ or tissue. Further, the methods detailed herein may involve killing the at least one pathogen to formulate the antigenic composition as a whole killed pathogen composition. Further, and without limitation, the at least one pathogen may be a bacterium, a virus, a protozoa, a fungus, or a helminth.

Other Embodiments

Although various embodiments of the invention are disclosed herein, many adaptations and modifications may be made within the scope of the invention in accordance with the common general knowledge of those skilled in this art. Such modifications include the substitution of known equivalents for any aspect of the invention in order to achieve the same result in substantially the same way. Numeric ranges are inclusive of the numbers defining the range. In the specification, the word “comprising” is used as an open-ended term, substantially equivalent to the phrase “including, but not limited to”, and the word “comprises” has a corresponding meaning. Citation of references herein shall not be construed as an admission that such references are prior art to the present invention. All publications are incorporated herein by reference as if each individual publication were specifically and individually indicated to be incorporated by reference herein and as though fully set forth herein. The invention includes all embodiments and variations substantially as hereinbefore described and with reference to the examples and drawings. 

What is claimed is:
 1. A method for treating a human patient having Crohn's disease, the method comprising: administering to a human patient, diagnosed as having Crohn's disease and exhibiting symptoms of Crohn's disease, intradermally or subcutaneously an amount of an antigenic formulation comprising whole killed Escherichia coli (E. coli) cells in successive doses given at a dosage interval of at least one hour, so that two or more doses are administered over a period from 4 days to 1 week, over a dosage duration of at least one week, wherein the amount of the antigenic formulation and duration of the administering is therapeutically effective to reduce or eliminate the symptoms of Crohn's disease in the human patient, wherein the whole killed E. coli cells are cells of an E. coli strain that is pathogenic in colon.
 2. The method of claim 1, wherein the dosage duration is at least two weeks.
 3. The method of claim 2, wherein the antigenic formulation is administered so that each dose is effective to cause a visible localized inflammatory immune response at an administration site.
 4. The method of claim 3, wherein the antigenic formulation is administered so that the visible localized inflammation at the administration site occurs within 1 to 48 hours.
 5. The method of claim 4, wherein the whole killed E. coli cells are cells of an E. coli strain collected from a patient with an E. coli colonic infection.
 6. The method of claim 4, wherein the antigenic formulation is administered subcutaneously every day, or every other day.
 7. The method of claim 1, wherein the whole killed E. coli cells are cells of an E. coli strain collected from a patient with an E. coli colonic infection.
 8. The method of claim 7, wherein the dosage duration is at least two weeks.
 9. The method of claim 8, wherein the antigenic formulation is administered so that each dose is effective to cause a visible localized inflammatory immune response at an administration site.
 10. The method of claim 5, wherein the antigenic formulation is administered subcutaneously every day, or every other day.
 11. The method of claim 7, wherein the antigenic formulation is administered so that each dose is effective to cause a visible localized inflammatory immune response at an administration site.
 12. The method of claim 11, wherein the antigenic formulation is administered so that the visible localized inflammation at the administration site occurs within 1 to 48 hours.
 13. The method of claim 7, wherein the antigenic formulation is administered subcutaneously every day, or every other day.
 14. The method of claim 1, wherein the antigenic formulation is administered so that each dose is effective to cause a visible localized inflammatory immune response at an administration site.
 15. The method of claim 14, wherein the antigenic formulation is administered so that the visible localized inflammation at the administration site occurs within 1 to 48 hours.
 16. The method of claim 15, wherein the antigenic formulation is administered subcutaneously every day, or every other day. 